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Repository: https://github.com/Danis102/seqpac

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[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

Submitter: There are very few specific warnings/errors: for example that we don't have enough run-able examples, using too much of \donttest{}. But since our package depend on user provided references for best function, we cannot provide good examples with fully functional code all the time. We have, however, tried to provide as many self-sustained examples as possible. We hope that this is something reviewers may test and comment on during the review process, but we have tried to fix all R CMD checks and BioChecks as far as we can without disturbing package examples and fuctions

[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
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Sep 10 '21 14:09 Danis102

Hi @Danis102

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: seqpac
Type: Package
Title: seqpac - Group-based Analysis of Short Reads Using Sequence Counts
Version: 0.99.0
Authors@R: c(
    person("Daniel", "Natt", email="[email protected]", role= c("aut", "cre", "fnd")),
    person("Lovisa", "Örkenby", email="[email protected]", role= "ctb"),
    person("Signe", "Skog", email="[email protected]", role= "ctb"),
    person("Anita", "Öst", email="[email protected]", role= c("aut", "fnd"))
    )
Description: A collection of functions used for complete analysis of short sequenced reads. 
    The package was originally developed for small RNA analysis, but can be implemented on 
    any sequencing raw data (provided as a fastq-file) where intended unit of measurement 
    is counts of unique sequences. The core of the seqpac workflow is the generation and 
    subsequence analysis/visualization of a standardized list object called PAC. Using an 
    innovative target system, seqpac extracts, analyze and visualize group differences 
    using the PAC object.
    A PAC object in its most basic form is a list containing three types of data frames: 
    - Phenotype table (P): Sample names (rows) with associated metadata (columns) e.g. groups. 
    - Annotation table (A): Unique sequences (rows) with annotation (columns), eg. reference alignment.     
    - Counts table (C): Counts of unique sequences (rows) for each sample (columns).
    The PAC list-objects follow the rule:
    - Row names in P must be identical with column names in C.
    - Row names in A must be identical with row names in C.
    Thus P and A describes the columns and rows in C, respectively. The targeting system, will either 
    target specific samples in P (pheno_target) or sequences in A (anno_target) and group them according 
    to a target column in P and A, respectively.
License: GLP-3 + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
URL: https://github.com/Danis102/seqpac
BugReports: https://github.com/Danis102/seqpac/issues
biocViews: 
  Workflow 
  EpigeneticWorkflow 
  AnnotationWorkflow 
  GeneExpressionWorkflow
Depend:
  Biostrings (>= 2.46.0),
  foreach (>= 1.5.1),
  GenomicRanges (>= 1.30.3,
  Rbowtie (>= 1.18.0),
  ShortRead (>= 1.36.1),
  tibble (>= 3.1.2)
Imports:
  BiocParallel (>= 1.12.0),
  Biostrings (>= 2.46.0),
  cowplot (>= 0.9.4),
  data.table (>= 1.14.0),
  digest (>= 0.6.27),
  doParallel (>= 1.0.16),
  dplyr (>= 1.0.6),
  factoextra (>= 1.0.7),
  FactoMineR (>= 1.41),
  foreach (>= 1.5.1),
  GenomicRanges (>= 1.30.3),
  ggplot2 (>= 3.3.3),
  IRanges (>= 2.12.0),
  parallel (>= 3.4.4),
  Rbowtie (>= 1.18.0),
  readr (>= 1.4.0),
  reshape2 (>= 1.4.4),
  rtracklayer (>= 1.38.3),  
  ShortRead (>= 1.36.1),
  stringr (>= 1.4.0),
  stats (>= 3.4.4),
  tibble (>= 3.1.2),
  tidyr (>= 1.1.3)
Suggests:
  benchmarkme (>= 0.6.0),
  DESeq2 (>= 1.18.1),
  GenomeInfoDb (>= 1.14.0),  
  gginnards (>= 0.0.2),
  knitr,
  qqman (>= 0.1.8),
  rmarkdown,
  testthat,
  UpSetR (>= 1.4.0),
  venneuler
VignetteBuilder: 
  knitr

Sep 10 '21 14:09 bioc-issue-bot

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

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Sep 22 '21 16:09 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Sep 22 '21 16:09 bioc-issue-bot

Please fix the errors and warnings to meet the requirement of review process. If you need any help, please let me known or ask help in develop mailing list.

Sep 28 '21 13:09 jianhong

@Danis102 may we expect and updated version of submission soon? We like to see movement within a 3-4 week time frame?

Nov 09 '21 18:11 lshep

Very soon. We're working on updating the vignette according to some updates in the functions following changes after running BioCheck. Hopefully, the new updates will be submitted in just a few days.

Regards, Daniel Natt (main developer of seqpac)

Skaffa Outlook för Androidhttps://aka.ms/ghei36

From: lshep @.> Sent: Tuesday, November 9, 2021 7:15:00 PM To: Bioconductor/Contributions @.> Cc: Daniel Nätt @.>; Mention @.> Subject: Re: [Bioconductor/Contributions] Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation (#2275)

@Danis102https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FDanis102&data=04%7C01%7Cdaniel.natt%40liu.se%7Cd43cd6c865204c3b360508d9a3acd8f3%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637720785040605493%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mv%2FKx7t73XjAx68df%2BoQYVrk9%2B4qah%2FayZQAukE9sdo%3D&reserved=0 may we expect and updated version of submission soon? We like to see movement within a 3-4 week time frame?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2275%23issuecomment-964409375&data=04%7C01%7Cdaniel.natt%40liu.se%7Cd43cd6c865204c3b360508d9a3acd8f3%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637720785040615490%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=2XbhRUrEWJEjnKLZa6qZiUR%2BwHVDBTMSm9jKnq1k7Fo%3D&reserved=0, or unsubscribehttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALLCUX2EDLIQC4IYFWNES5TULFQKJANCNFSM5DZM52BA&data=04%7C01%7Cdaniel.natt%40liu.se%7Cd43cd6c865204c3b360508d9a3acd8f3%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637720785040625485%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=zJujWDTLcyPPuQ7ofTmKpAFow%2BsS7PXn6CKhigyIsGo%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cdaniel.natt%40liu.se%7Cd43cd6c865204c3b360508d9a3acd8f3%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637720785040625485%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KzraAYRG8wIXQdJEeOjVSBG15111TFUgh7ZchrMCjjQ%3D&reserved=0 or Androidhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cdaniel.natt%40liu.se%7Cd43cd6c865204c3b360508d9a3acd8f3%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637720785040635480%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=RLuIvqRcv6LWMC10eOoltrKsKu5DXZx2tWiJmPGAQFg%3D&reserved=0.

Nov 09 '21 18:11 Danis102

We are temporarily closing this issue for inactivity as it has been another 2 weeks with no progress. When you are ready to submit changes please ask for the issue to be reopened to continue the review process.

Nov 24 '21 11:11 lshep

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for your interest in Bioconductor.

Nov 24 '21 11:11 bioc-issue-bot

Dear Ishep,

Would you please reopen our issue (submission) on Bioconducter. We are now ready to update our GitHub master and submit a new version of seqpac. I apologize for the delay. I can garantee that it is no lack in commitment, but rather that I have been struggling with a rather severe diagnosis during the autumn. We now have a branch of Seqpac, however, that goes through BioCheck and devtools::check without any errors or warnings. So, please, reopen our issue, so we can go on with it :).

Best regards, Main developer Daniel Nätt

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Från: lshep @.***> Skickat: onsdag 24 november 2021 12:51 Till: Bioconductor/Contributions Kopia: Daniel Nätt; Mention Ämne: Re: [Bioconductor/Contributions] (inactive) Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation (#2275)

We are temporarily closing this issue for inactivity as it has been another 2 weeks with no progress. When you are ready to submit changes please ask for the issue to be reopened to continue the review process.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2275%23issuecomment-977804185&data=04%7C01%7Cdaniel.natt%40liu.se%7Cd567d5cb0b0a46a00ed808d9af40b43a%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637733514707399055%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=OiHd9KcMreGWQDvz3%2FalwMgjS6y5zW6%2FIF0CNgvcDlE%3D&reserved=0, or unsubscribehttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALLCUXZHQNDJVXAMMAKNW7TUNTGSXANCNFSM5DZM52BA&data=04%7C01%7Cdaniel.natt%40liu.se%7Cd567d5cb0b0a46a00ed808d9af40b43a%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637733514707409050%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rXKFy1kfjbGF0HUlojF6EyHWEYKvIH%2BHMtwYKrShylE%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cdaniel.natt%40liu.se%7Cd567d5cb0b0a46a00ed808d9af40b43a%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637733514707419044%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=TpfwYlzV7TCX%2Bx4FoIN3U0dc9H9g4u7BT153IYQP2rc%3D&reserved=0 or Androidhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cdaniel.natt%40liu.se%7Cd567d5cb0b0a46a00ed808d9af40b43a%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637733514707429041%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=nQd4kx0av3i6q0unDvsqp1WwIFjhI3wWhDDTZtvqZ%2B4%3D&reserved=0.

Dec 10 '21 09:12 Danis102

Dear @Danis102 ,

We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.

Dec 10 '21 12:12 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 344d85383cd7a6490a7a19192e5fe32fcd80b8e0

Dec 10 '21 18:12 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Dec 13 '21 12:12 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 8b6237424ffed57a45546103351cb68a434b570d

Dec 14 '21 16:12 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Dec 14 '21 17:12 bioc-issue-bot

Package 'seqpac' Review

The package passed check and build. But there are several issues need to be addressed. Please fix the following issues first and I will review it again.

The DESCRIPTION file

[ ] Depends field is not found in DESCRIPTION.
[ ] R version is not clear in DESCRIPTION.
[ ] 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
[ ] Consider adding these automatically suggested biocViews: BasicWorkflow

The CITATION file

[ ] Citation file not in correct format
- Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding

Unacceptable files

[ ] unacceptable files present
- ./vignettes/seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.pdf
- ./vignettes/seqpac_-_A_guide_to_sRNA_analysis_using_sequence-based_counts.md

General package development

[ ] Size of individual files <= 5MB.
- installed size is 30.0Mb
  - sub-directories of 1Mb or more: o extdata 28.4Mb

Unit tests

[ ] .Rbuildignore file includes the 'tests' folder.
[ ] Got errors in unit tests

Error in system.file("extdata", "drosophila_sRNA_pac.Rdata", package = "seqpac", mustWork = TRUE): no file found Backtrace: █

├─base::load(...) test_PAC_preprocess.R:8:6
└─base::system.file(...) ── Failure (test_PAC_reanno_advanced_mapping.R:289:3): Testing reanno workflow ... ── grepl("Your chromosome names in", test_err) is not TRUE

Documentation

[ ] Vignette should use BiocStyle package for formatting.
[ ] Please include Bioconductor installation instructions using BiocManager.
[ ] Consider adding runnable examples to the following man pages which document exported objects: * import_reanno.Rd, * map_rangetype.Rd, * PAC_deseq.Rd, * PAC_trna.Rd, * tRNA_class.Rd
[ ] Usage of dontrun{} / donttest{} found in man page examples. * import_reanno.Rd * make_conv.Rd * make_cutadapt.Rd * map_rangetype.Rd * PAC_deseq.Rd * PAC_gtf.Rd * PAC_trna.Rd * simplify_reanno.Rd * tRNA_class.Rd

R code

[ ] no direct slot access with @ or slot() - accessors implemented and used. * In file R/make_trim.R: + at line 556 found ' fstq@sread <- Biostrings::DNAStringSet(trim_fastq)' + at line 560 found ' qual <- paste(Biostrings::quality(fstq@quality)) ' + at line 562 found ' fstq@quality <- ShortRead::FastqQuality(Biostrings::BStringSet(qual)) ' + at line 607 found ' logi_min <- Biostrings::width(fstq@sread) >= seq_range["min"]' + at line 608 found ' logi_max <- Biostrings::width(fstq@sread) <= seq_range["max"]' + at line 621 found ' enc <- Biostrings::encoding(fstq@quality) # Phred score translations' + at line 628 found ' fstq@quality)), enc_srch)' + at line 630 found ' fstq@quality)) >= quality["percent"]' * In file R/PAC_deseq.R: + at line 166 found ' res_DESeq2@elementMetadata@listData$description[2], ": ")[[1]][2]' * In file R/PAC_gtf.R: + at line 528 found ' gtf <- gtf_lst[[i]][olap@to, trg_cols]' + at line 533 found ' splt <- split(gtf, as.factor(olap@from))' * In file R/seqpac_generics_methods.R: + at line 64 found 'pheno.PAC <- function(object){ object@Pheno }' + at line 73 found ' object@Pheno <- value' + at line 125 found 'anno.PAC <- function(object){ object@Anno }' + at line 135 found ' object@Anno <- value' + at line 190 found 'counts.PAC <- function(object){ object@Counts }' + at line 199 found ' object@Counts <- value' + at line 249 found 'norm.PAC <- function(object){ object@norm }' + at line 259 found ' object@norm <- value' + at line 307 found 'summary.PAC <- function(object){ object@summary }' + at line 317 found ' object@norm <- value' + at line 426 found 'rownames.PAC <- function(x){ rownames(x@Counts) }' + at line 461 found 'colnames.PAC <- function(x){colnames(x@Counts)}' + at line 531 found 'ncol.PAC <- function(x){ ncol(x@Counts) }' + at line 565 found 'nrow.PAC <- function(x){ nrow(x@Counts) }' + at line 674 found 'overview.reanno <- function(object){ object@Overview }' + at line 683 found ' object@Overview <- value' + at line 759 found 'full.reanno <- function(object){object@Full_anno} ' + at line 769 found ' object@Full_anno <- value' + at line 840 found 'rownames.reanno <- function(x){ dplyr::pull(x@Overview[1])}' + at line 856 found 'nrow.reanno <- function(x){ nrow(x@Overview) } ' * In file R/seqpac_S4classes.R: + at line 121 found ' pac <- list(Pheno=from@Pheno,' + at line 122 found ' Anno=from@Anno,' + at line 123 found ' Counts=from@Counts)' + at line 125 found ' if(!is.null(from@norm[[1]])){' + at line 126 found ' pac <- c(pac, list(norm= from@norm))' + at line 128 found ' if(!is.null(from@summary[[1]])){' + at line 129 found ' pac <- c(pac, list(summary= from@summary))' + at line 198 found ' pac@norm <- from$norm' + at line 201 found ' pac@summary <- from$summary' + at line 344 found ' seq_nam <- dplyr::pull(object@Overview[1])' + at line 345 found ' test1 <- lapply(object@Full_anno, function(y){' + at line 350 found ' test2 <- lapply(object@Full_anno, function(y){' + at line 357 found ' "\nPlease check @Full_anno tables:\n",' + at line 361 found ' return(cat("\n@Full_anno is not a tibble.",' + at line 362 found ' "\nPlease check @Full_anno tables:\n",' + at line 373 found ' rn <- list(Overview=from@Overview, ' + at line 374 found ' Full_anno=from@Full_anno)' * In file R/tRNA_class.R: + at line 168 found ' reference_length <- x$Ref_seq@ranges@width' + at line 169 found ' ref_name <- x$Ref_seq@ranges@NAMES'
[ ] incomplete final line found on * 'R/filtsep_bin.R' * 'R/make_conv.R' * 'R/make_PAC.R' * 'R/map_rangetype.R' * 'R/merge_lanes.R' * 'R/PAC_filtsep.R' * 'R/simplify_reanno.R'
[ ] is() or inherits() instead of class().
- In file R/PAC_check.R:
  - at line 95 found ' if(class(sample_check) %in% c("data.frame", "matrix")){'
  - at line 165 found ' if(class(seq_check) %in% c("data.frame", "matrix")){'
- In file R/PAC_gtf.R:
  - at line 286 found ' logi_fl <- "tbl_df" %in% class(gtf_lst[[i]]) '
- In file R/PAC_mapper.R:
  - at line 275 found ' grepl("DNAString", class(full))|'
  - at line 435 found ' class(fin_lst) <- c("list", "seqpac_map")'
[ ] system2 instead of system.
- In file R/make_cutadapt.R:
  - at line 188 found ' log_lst[[1]] <- system(paste0("cutadapt ", parse[[1]], '
  - at line 193 found ' log_lst[[2]] <- system(paste0("fastq_quality_filter ", '
- In file R/map_reanno.R:
  - at line 334 found ' basename(utils::capture.output(system("bowtie --version", '
  - at line 377 found ' system(bwt_exp, intern=FALSE, ignore.stderr=FALSE)'
[ ] message(), warning, stop instead of cat.
- In file R/add_reanno.R:
  - at line 232 found ' cat(paste0("\nSequences in total: ", length(seq_nam)))'
  - at line 235 found ' cat("\n")'
  - at line 243 found ' cat("\nExtracting genome(s) ...")'
  - at line 263 found ' cat(paste0("\n\tmis", i-1, "\t", cat_nam,"\t", cat_hits)) '
  - at line 295 found ' cat("\n\nCompiling everything into one table ...")'
  - at line 315 found ' cat("\nExtracting biotype(s) ...")'
  - at line 367 found ' cat("\n")'
  - at line 406 found ' cat(paste0("\n\tmis", i-1, "\t", cat_nam,"\tRef_hits=", '
  - at line 417 found ' cat("\nCompiling everything into one table ...")'
  - at line 466 found ' cat("\nMerging with PAC ...")'
- In file R/import_reanno.R:
  - at line 100 found ' cat("\n|--- Found", sum(form_logi), '
  - at line 108 found ' cat(paste0("\n |--- Import and reorganize ", basename(files)[k]))'
  - at line 148 found ' cat(paste0("\n |---> Generating minimum report ..."))'
  - at line 156 found ' cat("\n |---> Generating full report (please wait)...")'
  - at line 213 found ' cat(paste0("\n |---> ", nam, " done"))'
- In file R/make_conv.R:
  - at line 118 found ' cat("\nReading reference A ...")'
  - at line 129 found ' cat("\nReading reference B ...")'
  - at line 140 found ' cat("\nReading reference C ...")'
  - at line 152 found ' cat("\nMatching sequences in reference A vs B ...")'
  - at line 187 found ' cat("\nMatching sequences in reference A vs C ...")'
  - at line 222 found ' cat("\nGenerating final conversion table ...")'
  - at line 304 found ' cat("\n")'
- In file R/make_counts.R:
  - at line 228 found ' cat("Started at ", paste0(Sys.time()), "\n")'
  - at line 241 found ' cat("\nInput type was set to already trimmed fastq.")'
  - at line 243 found ' cat("\nInput type was set to untrimmed fastq.")'
  - at line 245 found ' cat("\nThe following fastq files were found in the path:\n")'
  - at line 263 found ' cat("\nSeqpac trimming using the make_cutadapt function was specified.")'
  - at line 264 found ' cat("\n--- Temporary trimmed fastq are stored in: ", paste0(output))'
  - at line 265 found ' cat("\n--- Unless moved, these will be removed when system restarts.")'
  - at line 266 found ' cat("\n--- Please run 'make_cutadapt' for more options.")'
  - at line 283 found ' cat("\n--- Default trimming:\n ")'
  - at line 284 found ' cat("\n---------------------------------------------")'
  - at line 285 found ' cat("\ncutadapt command:\n")'
  - at line 287 found ' cat("\n---------------------------------------------")'
  - at line 288 found ' cat("\nfastq_quality_filter command:\n")'
  - at line 290 found ' cat("\n\n")'
  - at line 312 found ' cat("\nSeqpac trimming using the make_trim function was specified.")'
  - at line 313 found ' cat("\n--- Temporary trimmed fastq are stored in: ", paste0(output))'
  - at line 314 found ' cat("\n--- Unless moved, these will be removed when system restarts.")'
  - at line 315 found ' cat("\n--- Please run 'make_trim' separately for more storage options.\n")'
  - at line 334 found ' cat("\nDefault trimming: \n")'
  - at line 335 found ' cat("----------------------------------------------")'
  - at line 336 found ' cat("\nadapt_3: \n")'
  - at line 337 found ' cat(parse$adapt_3, "\n")'
  - at line 339 found ' cat("----------------------------------------------")'
  - at line 340 found ' cat("\npoly G: \n")'
  - at line 342 found ' cat("----------------------------------------------")'
  - at line 343 found ' cat("\nsize filter:\n")'
  - at line 345 found ' cat("----------------------------------------------")'
  - at line 346 found ' cat("\nquality filter:\n")'
  - at line 348 found ' cat("----------------------------------------------\n")'
  - at line 385 found ' cat("\n\nIdentifying unique sequences in trimmed fastq files ...")'
  - at line 422 found ' cat("\nCompiling unique sequences ...")'
  - at line 454 found ' cat(paste0("\nYou specified evidence=NULL. All sequences will be saved...",'
  - at line 471 found ' cat(paste0("\nMaking a count table with sequences appearing in at least ", '
  - at line 475 found ' cat(paste0("\nAlso saves sequences with less evidence but >= ", '
  - at line 477 found ' cat(paste0('
  - at line 514 found ' cat("\nFinalizing at ", paste0(Sys.time()), "\n")'
- In file R/make_cutadapt.R:
  - at line 142 found ' cat("\nRunning make_cutadapt (R may stop responding) ...")'
  - at line 143 found ' cat("\n--- cutadapt and fastq_quality_filter must be correctly installed.")'
- In file R/make_pheno.R:
  - at line 229 found ' cat("Of", length(colnames(counts)), '
  - at line 234 found ' cat("\nNote, partial name matching was done.")'
  - at line 236 found ' cat("\n")'
  - at line 244 found ' cat("\nProgress report was specified, will attempt to match rownames...\n")'
  - at line 264 found ' cat("\n")'
  - at line 269 found ' cat("Done!\n")'
- In file R/make_reanno.R:
  - at line 222 found ' cat("\n\nReorganizing and matching reannotation files with PAC ...\n")'
  - at line 281 found ' cat("\nGenerating the overview file ...\n")'
  - at line 314 found ' cat("\nChecking the last anno_mis fasta file.\n")'
  - at line 334 found ' cat("Congratulation, all sequences recieved an annotation.\n")'
  - at line 338 found ' cat("Of the ", sum(logi_no_anno), '
  - at line 340 found ' cat(paste0("files ", perc, "% were found in ", file_nam, ".\n"))'
  - at line 348 found ' cat("Passed fasta check!\n")'
- In file R/make_trim.R:
  - at line 231 found ' cat("\nChecking trimming memory usage with benchmarkme...")'
  - at line 236 found ' cat(paste0('
  - at line 240 found ' cat("\n--- Heavy trimming processes needs approx.",'
  - at line 250 found ' cat(paste0("\n--- Worst scenario maximum system", '
  - at line 266 found ' cat(paste0("\n--- Trimming check passed.\n"))'
  - at line 300 found ' cat("\nNow entering the parallel trimming loop (R may stop respond) ...")'
  - at line 301 found ' cat(paste0("\n(progress may be followed in: ", output, ")"))'
- In file R/map_rangetype.R:
  - at line 335 found ' cat("\nIt seems the map object, but not the ss object, contains only",'
  - at line 350 found ' cat("\n")'
  - at line 356 found ' cat("\nThe following reference(s) will therefore be",'
- In file R/map_reanno.R:
  - at line 291 found ' cat("\n")'
  - at line 326 found ' cat("\nR internal mapping using the Rbowtie package was specified.\n")'
  - at line 327 found ' cat(paste0("This package uses bowtie version ", vrs, ".\n"))'
  - at line 328 found ' cat("If you need a newer version, please install Bowtie manually\n")'
  - at line 329 found ' cat("outside R and then use option type='external'.\n")'
  - at line 336 found ' cat("\nR external mapping depends on correct installation of bowtie.")'
  - at line 337 found ' cat("\nIf there are problems using external bowtie, try type='internal'.")'
  - at line 338 found ' cat(paste0("\nAn external bowtie installation was found using version", '
  - at line 343 found ' cat(paste0("\n\n******************************************************"))'
  - at line 344 found ' cat(paste0("\n|--- Mismatch ", mis_lst[[i]], '
  - at line 346 found ' cat("\n|--- Bowtie mapping:")'
  - at line 350 found ' cat("\n |--->", paste0(names(ref_paths)[j], "..."))'
  - at line 360 found ' cat("\n\n")'
  - at line 373 found ' cat("\n\n")'
  - at line 406 found ' if(any(rm_no_hits)){cat(paste0("\n\n|--- All reference but ", '
  - at line 409 found ' }else{cat(paste0("\n|--- All reference generated hits"))}'
  - at line 410 found ' cat(paste0("\n|--- Mismatch ", mis_lst[[i]], " finished -----|"))'
  - at line 412 found ' cat(paste0("\n\n******************************************************"))'
  - at line 413 found ' cat(paste0("\nCleaning up ... "))'
  - at line 418 found ' cat(paste0("\nReanno mapping finished at: ", format(Sys.time(), "%X")))'
  - at line 419 found ' cat(paste0("\nOutput files are saved in:\n ", paste0(output_path)))'
- In file R/PAC_covplot.R:
  - at line 209 found ' cat(paste0("\nOf ", '
  - at line 214 found ' cat(paste0("by one or more query sequence in PAC.\n"))'
  - at line 217 found ' cat("References with no coverage will be ignored.\n")'
  - at line 220 found ' cat("These reference names was not covered by any query sequence:\n")'
- In file R/PAC_deseq.R:
  - at line 120 found ' cat("\n")'
  - at line 167 found ' cat("\n")'
  - at line 168 found ' cat("\n")'
  - at line 169 found ' cat(paste0("** ", comp, " **"))'
  - at line 170 found ' cat("\n")'
  - at line 173 found ' test <- try(cat(DESeq2::summary(res_DESeq2)), silent = TRUE)'
  - at line 175 found ' #cat(DESeq2::summary.DESeqResults(res_DESeq2))'
  - at line 176 found ' cat(DESeq2::DESeqResults(res_DESeq2))'
- In file R/PAC_filter.R:
  - at line 132 found ' cat(paste0("\n-- Pheno target was specified, will retain: ", '
  - at line 177 found ' cat(paste0("\n-- Anno target was specified, will retain: ", '
  - at line 205 found ' cat(paste0("\n-- Size filter will retain: ", '
  - at line 218 found ' cat("\n-- Count filter was specified.")'
  - at line 221 found ' cat(paste0("\n-- Filter on normalized (", '
  - at line 286 found ' cat("\n!! !!\nUser input needed:\n") '
  - at line 298 found ' cat(paste0("\n-- The chosen filters will retain: ", '
- In file R/PAC_gtf.R:
  - at line 268 found ' cat("\nImporting gtf files ...")'
  - at line 318 found ' cat("\nNo genome fasta was found, will atempt", '
  - at line 325 found ' cat("\nInput genome was an existing file. Will treat it as a",'
  - at line 397 found ' cat("\n\nReorganizing coordinates ...")'
  - at line 422 found ' cat("\n\nChromosome names compatibility check ...")'
  - at line 438 found ' cat("\n")'
  - at line 449 found ' cat("\n")'
  - at line 450 found ' cat('
  - at line 460 found ' cat("\n\nAnnotating against the gtf file(s) ...")'
  - at line 511 found ' cat(paste0("\n |--> Extract and compile '", gtf_nam, "' ...")) '
  - at line 554 found ' cat("\n\n")'
  - at line 558 found ' cat("\rGenerating full annotation list: ", i, "/", loop)'
  - at line 570 found ' cat("\n\n")'
  - at line 574 found ' cat("\rGenerating simplified annotation table: ", i, "/", loop)'
- In file R/PAC_mapper.R:
  - at line 225 found ' cat("\nImporting reference from DNAStringSet ...")'
  - at line 229 found ' cat("\nReading reference from fasta file ...")'
  - at line 233 found ' cat("\nTry to import reference from character vector ...")'
  - at line 272 found ' cat("\nBowtie indexes found. Will try to use them...")'
  - at line 277 found ' cat("\nNo bowtie indexes.")'
  - at line 278 found ' cat("\nWill try to reindex references ...")'
- In file R/PAC_nbias.R:
  - at line 149 found ' cat(paste0("\nCounting nucleotides"))'
- In file R/PAC_saturation.R:
  - at line 70 found ' cat("\nOrganizing data...\n") '
  - at line 78 found ' cat(paste0("\nPermutations will be generated using ", threads, " of ", parallel::detectCores(), " available core workers.")) '
  - at line 79 found ' cat(paste0("\nMaking ", resample, " permutations at ", steps," equally distributed sequence depths."))'
  - at line 80 found ' cat(paste0("\nData will be saved for two coverage thresholds at >= ", thresh[1], " counts and >= ", thresh[2], " counts\n")) '
  - at line 114 found ' cat("\nNow fitting the Asymptotic curve and plotting the results...\n")'
- In file R/PAC_trna.R:
  - at line 416 found ' return(cat("\nPaired samples are not yet implemented in the function,",'
- In file R/seqpac_generics_methods.R:
  - at line 366 found ' cat("PAC object with: \n")'
  - at line 367 found ' cat(" ", nrow(pac$Pheno), "samples\n")'
  - at line 368 found ' cat(" ",nrow(pac$Anno), "sequences\n")'
  - at line 374 found ' cat(paste0(" mean total counts: ", avg, " (min:", mn, "/max:", mx, ")\n"))'
  - at line 375 found ' cat(" best sequence:", mx_seq, "mean counts\n")'
  - at line 376 found ' cat(" worst sequence:", mn_seq, "mean counts\n")'
  - at line 378 found ' cat("normalized tables:", length(pac$norm),"\n")'
  - at line 379 found ' cat(names(pac$norm),"\n")'
  - at line 382 found ' cat("summarized tables:", length(pac$summary),"\n")'
  - at line 383 found ' cat(names(pac$summary),"\n")'
- In file R/seqpac_S4classes.R:
  - at line 356 found ' return(cat("\nSequence names are not identical.",'
  - at line 361 found ' return(cat("\n@Full_anno is not a tibble.",'
- In file R/simplify_reanno.R:
  - at line 328 found ' cat(paste0("\nNumber of mismatches specified by user: ", '
  - at line 351 found ' cat(paste0("\nBiotypes will be asigned as follows:\n"))'
- In file R/tRNA_class.R:
  - at line 156 found ' cat("The map object contains references without hits.",'
[ ] No paste in message(), warning, stop
- In file R/make_cutadapt.R:
  - at line 165 found ' stop(paste0('
- In file R/make_reanno.R:
  - at line 256 found ' warning(paste( "Missing references in Reanno file(s):\n", '
  - at line 321 found ' stop(paste0('
  - at line 343 found ' warning(paste0(" Not all missing annotations were found in ", '
- In file R/make_trim.R:
  - at line 278 found ' stop(paste0("\n There are files in the output folder:\n ", '
- In file R/map_reanno.R:
  - at line 293 found ' warning(paste0("\n There are files in the output folder:\n ", '
  - at line 299 found ' warning(paste0("\n There are files in the output folder:\n ", '
  - at line 305 found ' stop(paste0("Please move or delete the files in the output folder."))'
- In file R/PAC_check.R:
  - at line 58 found ' stop(paste0("\nSample names in Pheno (row names) and Counts",'
  - at line 62 found ' stop(paste0("\nSequence names in Anno (row names) and Counts",'
  - at line 98 found ' stop(paste0("\nSample (row) names in new table are not identical",'
  - at line 104 found ' stop(paste0("\nSample (column) names in new table are not identical",'
  - at line 120 found ' stop(paste0('
  - at line 129 found ' stop(paste0('
  - at line 192 found ' stop(paste0('
- In file R/PAC_summary.R:
  - at line 107 found ' stop(paste0("\nThere is no object called '", norm, "' in the norm list.",'
[ ] :: is not suggested in source code unless you can make sure all the packages are imported.
[ ] 1:n is not suggested in source code. Use seq_along or seq.int instead.
- In file R/add_reanno.R:
  - at line 246 found ' for (i in 1:(mismatches+1)){'
  - at line 251 found ' for (a in 1:length(full_lst)){'
  - at line 301 found ' for(z in 1:length(fin_lst)){'
  - at line 318 found ' for (i in 1:(mismatches+1)){'
  - at line 324 found ' for (a in 1:length(bio_search)){'
  - at line 445 found ' colsrch <- c("Mis0_bio", paste0("Mis0_bio", 1:100))'
  - at line 449 found ' colsrch <- c("Mis0_genome", paste0("Mis0_genome", 1:100))'
- In file R/filtsep_bin.R:
  - at line 70 found ' for(i in 1:length(filtsep_lst)){'
- In file R/import_reanno.R:
  - at line 107 found ' for (k in 1:length(files)){'
  - at line 171 found ' bowtie_out_lst[[k]] <- foreach::foreach(s=1:length(chnks_rng[[1]]), '
- In file R/make_conv.R:
  - at line 154 found ' for(i in 1:length(ref1_md5_vec)){'
  - at line 189 found ' for(i in 1:length(ref1_md5_vec)){'
  - at line 226 found ' for(i in 1:length(hits1)){'
  - at line 290 found ' for(i in 1:length(reference_list)){'
  - at line 292 found ' colnames(df)[1:length(reference_list)]))'
- In file R/make_counts.R:
  - at line 401 found ' seq_lst <- foreach::foreach(i=1:length(fls), .final = function(x){'
  - at line 487 found ' reads_lst <- foreach::foreach(i=1:length(fls),.final = function(x){'
  - at line 552 found ' stat_dt$sample <- paste0("fastq_", 1:length(stat_dt$sample))'
- In file R/make_cutadapt.R:
  - at line 178 found ' prog_report <- foreach::foreach(i=1:length(fls), '
- In file R/make_pheno.R:
  - at line 207 found ' for(i in 1:nrow(df)){'
  - at line 214 found ' for(i in 1:nrow(df)){'
- In file R/make_reanno.R:
  - at line 209 found ' seqs <- (seq(1:length(files)))-1'
  - at line 211 found ' for(i in 1:length(files)){'
  - at line 263 found ' for(j in 1:length(NA_which)){'
  - at line 268 found ' for(g in 1:length(NA_which[[j]])){'
  - at line 295 found ' for (bio in 1:bio_cat){'
- In file R/make_trim.R:
  - at line 248 found ' decreasing = TRUE)[1:par_ns])/1000000000'
  - at line 305 found ' i=1:length(fls), .inorder = TRUE, .export= c("nam_trim", "nam"),'
  - at line 414 found ' for(z in 1:length(start_gone)){'
  - at line 623 found ' names(enc))[paste0(enc) %in% as.character(1:quality["threshold"]-1)]'
  - at line 653 found ' for(i in 1:length(prog_report)){'
  - at line 666 found ' for(i in 1:length(prog_report)){'
- In file R/map_rangetype.R:
  - at line 193 found ' intervals=list(start=1:5, mid=45:55, end=95:100), '
  - at line 216 found ' for(i in 1:length(map)){'
  - at line 289 found ' for (i in 1:length(logi_breaks)){'
  - at line 376 found ' for(i in 1:nrow(fin_ss_df)){'
  - at line 441 found ' for (k in 1:nrow(code_split)){'
  - at line 447 found ' for (k in 1:nrow(code_split)){'
- In file R/map_reanno.R:
  - at line 342 found ' for(i in 1:length(mis_lst)){'
  - at line 349 found ' for (j in 1:length(ref_paths)){'
- In file R/merge_lanes.R:
  - at line 142 found ' done <- foreach::foreach(j=1:length(fls_nam)) %dopar% {'
  - at line 149 found ' for(i in 1:length(lns)){'
- In file R/PAC_check.R:
  - at line 116 found ' if(sum(grepl(paste(rownames(PAC$Pheno)[1:2], collapse="|"), '
  - at line 125 found ' if(sum(grepl(paste(rownames(PAC$Pheno)[1:2], collapse="|"), '
- In file R/PAC_covplot.R:
  - at line 232 found ' for(i in 1:length(multi_seq_lst)){'
  - at line 251 found ' for(i in 1:length(ref_data_lst)){'
  - at line 275 found ' for(i in 1:length(sub_map)){'
  - at line 281 found ' cov_lst[[i]] <- lapply(as.list(1:length(summary_target[[2]])), function(x){'
  - at line 285 found ' Position=as.factor(1:IRanges::width(sub_map[[i]]$Ref_seq)), '
  - at line 293 found ' fin <- data.frame(Position=ordered(as.factor(1:length(cov))), '
  - at line 314 found ' for(i in 1:length(cov_lst)){'
- In file R/PAC_deseq.R:
  - at line 133 found ' for (i in 1:length(cols)){'
- In file R/PAC_filter.R:
  - at line 252 found ' for (i in 1:length(filt_plot$x_graph)){ '
- In file R/PAC_gtf.R:
  - at line 265 found ' names(gtf) <- 1:length(gtf)'
  - at line 283 found ' for (i in 1:length(gtf_lst)){'
  - at line 402 found ' for(i in 1:nrow(mis_genome)){'
  - at line 427 found ' for(i in 1:length(gtf_lst)){'
  - at line 478 found ' coord_gr <- foreach::foreach(i=1:length(coord_lst), '
  - at line 509 found ' for(i in 1:length(gtf_gr)){'
  - at line 515 found ' coord_anno <- foreach::foreach(t=1:length(coord_gr), '
  - at line 557 found ' for(i in 1:loop){'
  - at line 561 found ' for(z in 1:length(anno_lst)){'
  - at line 573 found ' for(i in 1:loop){'
  - at line 577 found ' for(z in 1:length(anno_lst)){'
- In file R/PAC_jitter.R:
  - at line 167 found ' plt_lst <- as.list(1:ncol(df))'
- In file R/PAC_mapper.R:
  - at line 309 found ' for(i in 1:length(align_lst)){'
  - at line 369 found ' for(i in 1:length(align_lst)){'
  - at line 407 found ' positions_lst <- foreach::foreach(j=1:length(algn_lst), '
- In file R/PAC_nbias.R:
  - at line 184 found ' for(i in 1:length(nuc_lst)){'
- In file R/PAC_norm.R:
  - at line 61 found ' for (i in 1:length(lib_sizes)){'
- In file R/PAC_pca.R:
  - at line 124 found ' colnames(data) <- paste(labels, 1:ncol(data), sep="_")'
- In file R/PAC_pie.R:
  - at line 166 found ' for(i in 1:length(x)){'
  - at line 180 found ' for (i in 1:length(tot_cnts)){ '
  - at line 192 found ' bio <- bio[c(extra, (1:length(bio))[!1:length(bio) %in% extra])] '
- In file R/PAC_saturation.R:
  - at line 81 found ' resampl_sub_lst <- foreach::foreach(i=1:length(x_vect), .inorder=FALSE) %dopar% {'
  - at line 95 found ' for(t in 1:length(thresh)){'
  - at line 159 found ' names(plots) <- paste("thresh", 1:length(thresh), sep="_")'
- In file R/PAC_sizedist.R:
  - at line 173 found ' for(i in 1:length(anno_target[[2]])){ '
  - at line 196 found ' for(i in 1:length(size_lst)){'
- In file R/PAC_stackbar.R:
  - at line 152 found ' for(i in 1:length(x)){'
  - at line 166 found ' for (i in 1:length(tot_cnts)){ '
- In file R/PAC_summary.R:
  - at line 144 found ' combn_lst <- as.list(data.frame(utils::combn(1:length(sub_data_lst),m = 2)))'
- In file R/PAC_trna.R:
  - at line 312 found ' df <- df[rep( 1:length(missing), times=length(unique(y$variable))),]'
  - at line 332 found ' ordr <- ordr[1:top] # Extract the top '
- In file R/simplify_reanno.R:
  - at line 301 found ' if(sum(names(input)[1:3] == c("Pheno", "Anno", "Counts"))==3){'
  - at line 363 found ' Hierarchy=1:(nrow(catg)), '
  - at line 381 found ' for(i in 1:length(search_terms)){'
[ ] Vectorize: no unnecessary for loops present.
- In file R/add_reanno.R:
  - at line 246 found ' for (i in 1:(mismatches+1)){'
  - at line 251 found ' for (a in 1:length(full_lst)){'
  - at line 301 found ' for(z in 1:length(fin_lst)){'
  - at line 318 found ' for (i in 1:(mismatches+1)){'
  - at line 324 found ' for (a in 1:length(bio_search)){'
- In file R/filtsep_bin.R:
  - at line 70 found ' for(i in 1:length(filtsep_lst)){'
- In file R/import_reanno.R:
  - at line 107 found ' for (k in 1:length(files)){'
- In file R/make_conv.R:
  - at line 154 found ' for(i in 1:length(ref1_md5_vec)){'
  - at line 189 found ' for(i in 1:length(ref1_md5_vec)){'
  - at line 226 found ' for(i in 1:length(hits1)){'
  - at line 290 found ' for(i in 1:length(reference_list)){'
- In file R/make_pheno.R:
  - at line 207 found ' for(i in 1:nrow(df)){'
  - at line 214 found ' for(i in 1:nrow(df)){'
- In file R/make_reanno.R:
  - at line 211 found ' for(i in 1:length(files)){'
  - at line 263 found ' for(j in 1:length(NA_which)){'
  - at line 268 found ' for(g in 1:length(NA_which[[j]])){'
  - at line 295 found ' for (bio in 1:bio_cat){'
- In file R/make_trim.R:
  - at line 414 found ' for(z in 1:length(start_gone)){'
  - at line 653 found ' for(i in 1:length(prog_report)){'
  - at line 666 found ' for(i in 1:length(prog_report)){'
- In file R/map_rangetype.R:
  - at line 216 found ' for(i in 1:length(map)){'
  - at line 289 found ' for (i in 1:length(logi_breaks)){'
  - at line 376 found ' for(i in 1:nrow(fin_ss_df)){'
  - at line 441 found ' for (k in 1:nrow(code_split)){'
  - at line 447 found ' for (k in 1:nrow(code_split)){'
- In file R/map_reanno.R:
  - at line 342 found ' for(i in 1:length(mis_lst)){'
  - at line 349 found ' for (j in 1:length(ref_paths)){'
- In file R/merge_lanes.R:
  - at line 149 found ' for(i in 1:length(lns)){'
- In file R/PAC_covplot.R:
  - at line 232 found ' for(i in 1:length(multi_seq_lst)){'
  - at line 251 found ' for(i in 1:length(ref_data_lst)){'
  - at line 275 found ' for(i in 1:length(sub_map)){'
  - at line 314 found ' for(i in 1:length(cov_lst)){'
- In file R/PAC_deseq.R:
  - at line 133 found ' for (i in 1:length(cols)){'
- In file R/PAC_filter.R:
  - at line 252 found ' for (i in 1:length(filt_plot$x_graph)){ '
- In file R/PAC_gtf.R:
  - at line 283 found ' for (i in 1:length(gtf_lst)){'
  - at line 402 found ' for(i in 1:nrow(mis_genome)){'
  - at line 427 found ' for(i in 1:length(gtf_lst)){'
  - at line 509 found ' for(i in 1:length(gtf_gr)){'
  - at line 557 found ' for(i in 1:loop){'
  - at line 561 found ' for(z in 1:length(anno_lst)){'
  - at line 573 found ' for(i in 1:loop){'
  - at line 577 found ' for(z in 1:length(anno_lst)){'
- In file R/PAC_mapper.R:
  - at line 309 found ' for(i in 1:length(align_lst)){'
  - at line 369 found ' for(i in 1:length(align_lst)){'
- In file R/PAC_nbias.R:
  - at line 184 found ' for(i in 1:length(nuc_lst)){'
- In file R/PAC_norm.R:
  - at line 61 found ' for (i in 1:length(lib_sizes)){'
- In file R/PAC_pie.R:
  - at line 166 found ' for(i in 1:length(x)){'
  - at line 180 found ' for (i in 1:length(tot_cnts)){ '
- In file R/PAC_saturation.R:
  - at line 95 found ' for(t in 1:length(thresh)){'
- In file R/PAC_sizedist.R:
  - at line 173 found ' for(i in 1:length(anno_target[[2]])){ '
  - at line 196 found ' for(i in 1:length(size_lst)){'
- In file R/PAC_stackbar.R:
  - at line 152 found ' for(i in 1:length(x)){'
  - at line 166 found ' for (i in 1:length(tot_cnts)){ '
- In file R/simplify_reanno.R:
  - at line 381 found ' for(i in 1:length(search_terms)){'
[ ] Use file.path to replace paste
- In file R/make_counts.R:
  - at line 250 found ' output <- paste0(tempdir(), "/seqpac/")'
- In file R/map_reanno.R:
  - at line 317 found ' filepath=paste0(output_path, "/anno_mis0.fa"), '
  - at line 347 found ' input_file <- paste0(output_path, "/anno_mis", mis_lst[[i]], ".fa")'
  - at line 401 found ' save(reanno, file= paste0(output_path, "/Full_reanno_", suffix, ".Rdata"))'
- In file R/merge_lanes.R:
  - at line 145 found ' out_nam <- paste0(out_path, "/", fl_base, ".fastq.gz")'
- In file R/PAC_mapper.R:
  - at line 248 found ' outpath <- paste0(tempdir(), "/", "seqpac")'
  - at line 249 found ' ref_path <- paste0(tempdir(), "/ref/reference.fa")'
[ ] Avoid redundant 'stop' and 'warn*' in signal conditions. Found in files: * R/PAC_filter.R (line 114, column 11) * R/PAC_filter.R (line 227, column 12) * R/PAC_filter.R (line 230, column 12) * R/PAC_gtf.R (line 389, column 5)
[ ] Avoid 'suppressWarnings'/'*Messages' if possible (found 13 times) * in R/make_conv.R (line 293, column 7) * in R/make_counts.R (line 253, column 7) * in R/make_cutadapt.R (line 153, column 5) * in R/make_trim.R (line 285, column 5) * in R/map_reanno.R (line 309, column 5) * in R/PAC_filter.R (line 259, column 7) * in R/PAC_gtf.R (line 370, column 13) * in R/PAC_gtf.R (line 527, column 17) * in R/PAC_mapper.R (line 253, column 3) * in R/PAC_mapper.R (line 257, column 3) * in R/PAC_pca.R (line 105, column 12) * in R/PAC_pca.R (line 109, column 12) * in R/PAC_trna.R (line 466, column 9)
[ ] Function arguments are tested for validity.
[ ] Functional programming: code repetition. eg repetition in colnames and rownames

mailing list

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Dec 21 '21 00:12 jianhong

@Danis102 may we expect any updates soon? We like to see reviews move forward within 3-4 weeks.

Jan 20 '22 16:01 lshep

Please have patience. It has been Christmas, New Year, Covid-restrictions and sick leaves in the lab that have prevented us to work as much as we would have wanted. But rest assured that we are working as much as we can. I hope that you will have a new update during next week.

From: lshep @.> Sent: Thursday, January 20, 2022 5:38 PM To: Bioconductor/Contributions @.> Cc: Daniel Nätt @.>; Mention @.> Subject: Re: [Bioconductor/Contributions] Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation (#2275)

@Danis102https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FDanis102&data=04%7C01%7Cdaniel.natt%40liu.se%7C7b98556d891c4ed6ac4008d9dc3340fb%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637782934971615911%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=fn3cvRnXBreteS%2FRdgIA4VPyQg%2F4Gpwe%2B1rgN1NCZgg%3D&reserved=0 may we expect any updates soon? We like to see reviews move forward within 3-4 weeks.

Reply to this email directly, view it on GitHubhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F2275%23issuecomment-1017695791&data=04%7C01%7Cdaniel.natt%40liu.se%7C7b98556d891c4ed6ac4008d9dc3340fb%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637782934971615911%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=tyoT4iLdXjrFtm8W85aH0HVLrQekm%2FWhjEwelRSVUEo%3D&reserved=0, or unsubscribehttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALLCUX2OKKCA5Q7YO55SFE3UXA27JANCNFSM5DZM52BA&data=04%7C01%7Cdaniel.natt%40liu.se%7C7b98556d891c4ed6ac4008d9dc3340fb%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637782934971615911%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=oIjM4qirPFPwrak%2F0R7uDOBhNug0G41QassVIPUN98Q%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cdaniel.natt%40liu.se%7C7b98556d891c4ed6ac4008d9dc3340fb%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637782934971615911%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=sYmusmmh2ZD6Nho25m4JYzd6%2Fg7kJL9MTMfsEiNVePI%3D&reserved=0 or Androidhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cdaniel.natt%40liu.se%7C7b98556d891c4ed6ac4008d9dc3340fb%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637782934971615911%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=TG3quGc1YPiSq6AbukqH8PzriBoWr4m6OjGQ0FDyVyQ%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.@.>>

Jan 21 '22 10:01 Danis102

Received a valid push on git.bioconductor.org; starting a build for commit id: 7ecb616d932c020e89b93e18970c832bb17d49b4

Feb 01 '22 17:02 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, TIMEOUT". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Feb 01 '22 17:02 bioc-issue-bot

Dear reviewer, First we like thank you for the valuable comment. We have now made another bump, upload upstream of master, and tried to commit all suggestions and comments as far as we could.

Devtools::check() now runs without neither Errors, Warnings or Notes on our systems

BiocCheck::BiocCheck() runs without Errors and Warnings, but still report a few Notes related suggestions to the code. These were also commented by the reviewer in the latest issue/email. Attached you will find our responses to why it is important for us to avoid committing these suggestions to the code at this point. Since theses notes/comment are suggestions in nature, and not seem to be obligatory for admission to Bioconductor, but may instead seriously affect our workflows unless extensive testing is performed, we hope to address these notes/comments progressively at later updates of seqpac. Please, again, read our response in the attached document.

Yours sincerely, Daniel Nätt

From: JIANHONG OU @.> Sent: Tuesday, December 21, 2021 1:57 AM To: Bioconductor/Contributions @.> Cc: Daniel Nätt @.>; Mention @.> Subject: Re: [Bioconductor/Contributions] Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation (#2275)

Package 'seqpac' Review

The package passed check and build. But there are several issues need to be addressed. Please fix the following issues first and I will review it again.

The DESCRIPTION file

[ ] Depends field is not found in DESCRIPTION.
[ ] R version is not clear in DESCRIPTION.
[ ] 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
[ ] Consider adding these automatically suggested biocViews: BasicWorkflow

The CITATION file

[ ] Citation file not in correct format * Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding

Unacceptable files

[ ] unacceptable files present * ./vignettes/seqpac_-A_guide_to_sRNA_analysis_using_sequence-based_counts.pdf * ./vignettes/seqpac-_A_guide_to_sRNA_analysis_using_sequence-based_counts.md

General package development

[ ] Size of individual files <= 5MB. * installed size is 30.0Mb
- sub-directories of 1Mb or more: o extdata 28.4Mb

Unit tests

[ ] .Rbuildignore file includes the 'tests' folder.
[ ] Got errors in unit tests

Error in system.file("extdata", "drosophila_sRNA_pac.Rdata", package = "seqpac", mustWork = TRUE): no file found Backtrace: █

├─base::load(...) test_PAC_preprocess.R:8:6
└─base::system.file(...) ── Failure (test_PAC_reanno_advanced_mapping.R:289:3): Testing reanno workflow ... ── grepl("Your chromosome names in", test_err) is not TRUE

Documentation

[ ] Vignette should use BiocStyle package for formatting.
[ ] Please include Bioconductor installation instructions using BiocManager.
[ ] Consider adding runnable examples to the following man pages which document exported objects:
import_reanno.Rd,
map_rangetype.Rd,
PAC_deseq.Rd,
PAC_trna.Rd,
tRNA_class.Rd
- [ ] Usage of dontrun{} / donttest{} found in man page examples.
import_reanno.Rd
make_conv.Rd
make_cutadapt.Rd
map_rangetype.Rd
PAC_deseq.Rd
PAC_gtf.Rd
PAC_trna.Rd
simplify_reanno.Rd
tRNA_class.Rd

R code

[ ] no direct slot access with @ or slot() - accessors implemented and used.
In file R/make_trim.R:

at line 556 found ' @.*** <- Biostrings::DNAStringSet(trim_fastq)'
at line 560 found ' qual <- @.***)) '
at line 562 found ' @.*** <- ShortRead::FastqQuality(Biostrings::BStringSet(qual)) '
at line 607 found ' logi_min <- @.***) >= seq_range["min"]'
at line 608 found ' logi_max <- @.***) <= seq_range["max"]'
at line 621 found ' enc <- @.***) # Phred score translations'
at line 628 found ' @.***)), enc_srch)'
at line 630 found ' @.***)) >= quality["percent"]'

In file R/PAC_deseq.R:

at line 166 found ' @.***@listData$description[2], ": ")[[1]][2]'

In file R/PAC_gtf.R:

at line 528 found ' gtf <- @.***, trg_cols]'
at line 533 found ' splt <- split(gtf, @.***))'

In file R/seqpac_generics_methods.R:

at line 64 found 'pheno.PAC <- function(object){ @.*** }'
at line 73 found ' @.*** <- value'
at line 125 found 'anno.PAC <- function(object){ @.*** }'
at line 135 found ' @.*** <- value'
at line 190 found 'counts.PAC <- function(object){ @.*** }'
at line 199 found ' @.*** <- value'
at line 249 found 'norm.PAC <- function(object){ @.*** }'
at line 259 found ' @.*** <- value'
at line 307 found 'summary.PAC <- function(object){ @.*** }'
at line 317 found ' @.*** <- value'
at line 426 found 'rownames.PAC <- function(x){ @.***) }'
at line 461 found 'colnames.PAC <- @.***)}'
at line 531 found 'ncol.PAC <- function(x){ @.***) }'
at line 565 found 'nrow.PAC <- function(x){ @.***) }'
at line 674 found 'overview.reanno <- function(object){ @.*** }'
at line 683 found ' @.*** <- value'
at line 759 found 'full.reanno <- @.***_anno} '
at line 769 found ' @.***_anno <- value'
at line 840 found 'rownames.reanno <- function(x){ @.***[1])}'
at line 856 found 'nrow.reanno <- function(x){ @.***) } '

In file R/seqpac_S4classes.R:

at line 121 found ' pac <- @.***,'
at line 122 found ' @.***,'
at line 123 found ' @.***)'
at line 125 found ' @.***[[1]])){'
at line 126 found ' pac <- c(pac, list(norm= @.***))'
at line 128 found ' @.***[[1]])){'
at line 129 found ' pac <- c(pac, list(summary= @.***))'
at line 198 found ' @.*** <- from$norm'
at line 201 found ' @.*** <- from$summary'
at line 344 found ' seq_nam <- @.***[1])'
at line 345 found ' test1 <- @.***_anno, function(y){'
at line 350 found ' test2 <- @.***_anno, function(y){'
at line 357 found ' "\nPlease check @Full_anno tables:\n",'
at line 361 found ' @.***_anno is not a tibble.",'
at line 362 found ' "\nPlease check @Full_anno tables:\n",'
at line 373 found ' rn <- @.***, '
at line 374 found ' @.***_anno)'

In file R/tRNA_class.R:

at line 168 found ' reference_length <- @.***@width'
at line 169 found ' ref_name <- @.***@NAMES'
- [ ] incomplete final line found on

'R/filtsep_bin.R'
'R/make_conv.R'
'R/make_PAC.R'
'R/map_rangetype.R'
'R/merge_lanes.R'
'R/PAC_filtsep.R'
'R/simplify_reanno.R'
- [ ] is() or inherits() instead of class().
- In file R/PAC_check.R: * at line 95 found ' if(class(sample_check) %in% c("data.frame", "matrix")){' * at line 165 found ' if(class(seq_check) %in% c("data.frame", "matrix")){'
- In file R/PAC_gtf.R: * at line 286 found ' logi_fl <- "tbl_df" %in% class(gtf_lst[[i]]) '
- In file R/PAC_mapper.R: * at line 275 found ' grepl("DNAString", class(full))|' * at line 435 found ' class(fin_lst) <- c("list", "seqpac_map")'
- [ ] system2 instead of system.
- In file R/make_cutadapt.R: * at line 188 found ' log_lst[[1]] <- system(paste0("cutadapt ", parse[[1]], ' * at line 193 found ' log_lst[[2]] <- system(paste0("fastq_quality_filter ", '
- In file R/map_reanno.R: * at line 334 found ' basename(utils::capture.output(system("bowtie --version", ' * at line 377 found ' system(bwt_exp, intern=FALSE, ignore.stderr=FALSE)'
- [ ] message(), warning, stop instead of cat.
- In file R/add_reanno.R: * at line 232 found ' cat(paste0("\nSequences in total: ", length(seq_nam)))' * at line 235 found ' cat("\n")' * at line 243 found ' cat("\nExtracting genome(s) ...")' * at line 263 found ' cat(paste0("\n\tmis", i-1, "\t", cat_nam,"\t", cat_hits)) ' * at line 295 found ' cat("\n\nCompiling everything into one table ...")' * at line 315 found ' cat("\nExtracting biotype(s) ...")' * at line 367 found ' cat("\n")' * at line 406 found ' cat(paste0("\n\tmis", i-1, "\t", cat_nam,"\tRef_hits=", ' * at line 417 found ' cat("\nCompiling everything into one table ...")' * at line 466 found ' cat("\nMerging with PAC ...")'
- In file R/import_reanno.R: * at line 100 found ' cat("\n|--- Found", sum(form_logi), ' * at line 108 found ' cat(paste0("\n |--- Import and reorganize ", basename(files)[k]))' * at line 148 found ' cat(paste0("\n |---> Generating minimum report ..."))' * at line 156 found ' cat("\n |---> Generating full report (please wait)...")' * at line 213 found ' cat(paste0("\n |---> ", nam, " done"))'
- In file R/make_conv.R: * at line 118 found ' cat("\nReading reference A ...")' * at line 129 found ' cat("\nReading reference B ...")' * at line 140 found ' cat("\nReading reference C ...")' * at line 152 found ' cat("\nMatching sequences in reference A vs B ...")' * at line 187 found ' cat("\nMatching sequences in reference A vs C ...")' * at line 222 found ' cat("\nGenerating final conversion table ...")' * at line 304 found ' cat("\n")'
- In file R/make_counts.R: * at line 228 found ' cat("Started at ", paste0(Sys.time()), "\n")' * at line 241 found ' cat("\nInput type was set to already trimmed fastq.")' * at line 243 found ' cat("\nInput type was set to untrimmed fastq.")' * at line 245 found ' cat("\nThe following fastq files were found in the path:\n")' * at line 263 found ' cat("\nSeqpac trimming using the make_cutadapt function was specified.")' * at line 264 found ' cat("\n--- Temporary trimmed fastq are stored in: ", paste0(output))' * at line 265 found ' cat("\n--- Unless moved, these will be removed when system restarts.")' * at line 266 found ' cat("\n--- Please run 'make_cutadapt' for more options.")' * at line 283 found ' cat("\n--- Default trimming:\n ")' * at line 284 found ' cat("\n---------------------------------------------")' * at line 285 found ' cat("\ncutadapt command:\n")' * at line 287 found ' cat("\n---------------------------------------------")' * at line 288 found ' cat("\nfastq_quality_filter command:\n")' * at line 290 found ' cat("\n\n")' * at line 312 found ' cat("\nSeqpac trimming using the make_trim function was specified.")' * at line 313 found ' cat("\n--- Temporary trimmed fastq are stored in: ", paste0(output))' * at line 314 found ' cat("\n--- Unless moved, these will be removed when system restarts.")' * at line 315 found ' cat("\n--- Please run 'make_trim' separately for more storage options.\n")' * at line 334 found ' cat("\nDefault trimming: \n")' * at line 335 found ' cat("----------------------------------------------")' * at line 336 found ' cat("\nadapt_3: \n")' * at line 337 found ' cat(parse$adapt_3, "\n")' * at line 339 found ' cat("----------------------------------------------")' * at line 340 found ' cat("\npoly G: \n")' * at line 342 found ' cat("----------------------------------------------")' * at line 343 found ' cat("\nsize filter:\n")' * at line 345 found ' cat("----------------------------------------------")' * at line 346 found ' cat("\nquality filter:\n")' * at line 348 found ' cat("----------------------------------------------\n")' * at line 385 found ' cat("\n\nIdentifying unique sequences in trimmed fastq files ...")' * at line 422 found ' cat("\nCompiling unique sequences ...")' * at line 454 found ' cat(paste0("\nYou specified evidence=NULL. All sequences will be saved...",' * at line 471 found ' cat(paste0("\nMaking a count table with sequences appearing in at least ", ' * at line 475 found ' cat(paste0("\nAlso saves sequences with less evidence but >= ", ' * at line 477 found ' cat(paste0(' * at line 514 found ' cat("\nFinalizing at ", paste0(Sys.time()), "\n")'
- In file R/make_cutadapt.R: * at line 142 found ' cat("\nRunning make_cutadapt (R may stop responding) ...")' * at line 143 found ' cat("\n--- cutadapt and fastq_quality_filter must be correctly installed.")'
- In file R/make_pheno.R: * at line 229 found ' cat("Of", length(colnames(counts)), ' * at line 234 found ' cat("\nNote, partial name matching was done.")' * at line 236 found ' cat("\n")' * at line 244 found ' cat("\nProgress report was specified, will attempt to match rownames...\n")' * at line 264 found ' cat("\n")' * at line 269 found ' cat("Done!\n")'
- In file R/make_reanno.R: * at line 222 found ' cat("\n\nReorganizing and matching reannotation files with PAC ...\n")' * at line 281 found ' cat("\nGenerating the overview file ...\n")' * at line 314 found ' cat("\nChecking the last anno_mis fasta file.\n")' * at line 334 found ' cat("Congratulation, all sequences recieved an annotation.\n")' * at line 338 found ' cat("Of the ", sum(logi_no_anno), ' * at line 340 found ' cat(paste0("files ", perc, "% were found in ", file_nam, ".\n"))' * at line 348 found ' cat("Passed fasta check!\n")'
- In file R/make_trim.R: * at line 231 found ' cat("\nChecking trimming memory usage with benchmarkme...")' * at line 236 found ' cat(paste0(' * at line 240 found ' cat("\n--- Heavy trimming processes needs approx.",' * at line 250 found ' cat(paste0("\n--- Worst scenario maximum system", ' * at line 266 found ' cat(paste0("\n--- Trimming check passed.\n"))' * at line 300 found ' cat("\nNow entering the parallel trimming loop (R may stop respond) ...")' * at line 301 found ' cat(paste0("\n(progress may be followed in: ", output, ")"))'
- In file R/map_rangetype.R: * at line 335 found ' cat("\nIt seems the map object, but not the ss object, contains only",' * at line 350 found ' cat("\n")' * at line 356 found ' cat("\nThe following reference(s) will therefore be",'
- In file R/map_reanno.R: * at line 291 found ' cat("\n")' * at line 326 found ' cat("\nR internal mapping using the Rbowtie package was specified.\n")' * at line 327 found ' cat(paste0("This package uses bowtie version ", vrs, ".\n"))' * at line 328 found ' cat("If you need a newer version, please install Bowtie manually\n")' * at line 329 found ' cat("outside R and then use option type='external'.\n")' * at line 336 found ' cat("\nR external mapping depends on correct installation of bowtie.")' * at line 337 found ' cat("\nIf there are problems using external bowtie, try type='internal'.")' * at line 338 found ' cat(paste0("\nAn external bowtie installation was found using version", ' * at line 343 found ' cat(paste0("\n\n******************************************************"))' * at line 344 found ' cat(paste0("\n|--- Mismatch ", mis_lst[[i]], ' * at line 346 found ' cat("\n|--- Bowtie mapping:")' * at line 350 found ' cat("\n |--->", paste0(names(ref_paths)[j], "..."))' * at line 360 found ' cat("\n\n")' * at line 373 found ' cat("\n\n")' * at line 406 found ' if(any(rm_no_hits)){cat(paste0("\n\n|--- All reference but ", ' * at line 409 found ' }else{cat(paste0("\n|--- All reference generated hits"))}' * at line 410 found ' cat(paste0("\n|--- Mismatch ", mis_lst[[i]], " finished -----|"))' * at line 412 found ' cat(paste0("\n\n******************************************************"))' * at line 413 found ' cat(paste0("\nCleaning up ... "))' * at line 418 found ' cat(paste0("\nReanno mapping finished at: ", format(Sys.time(), "%X")))' * at line 419 found ' cat(paste0("\nOutput files are saved in:\n ", paste0(output_path)))'
- In file R/PAC_covplot.R: * at line 209 found ' cat(paste0("\nOf ", ' * at line 214 found ' cat(paste0("by one or more query sequence in PAC.\n"))' * at line 217 found ' cat("References with no coverage will be ignored.\n")' * at line 220 found ' cat("These reference names was not covered by any query sequence:\n")'
- In file R/PAC_deseq.R: * at line 120 found ' cat("\n")' * at line 167 found ' cat("\n")' * at line 168 found ' cat("\n")' * at line 169 found ' cat(paste0("** ", comp, " **"))' * at line 170 found ' cat("\n")' * at line 173 found ' test <- try(cat(DESeq2::summary(res_DESeq2)), silent = TRUE)' * at line 175 found ' #cat(DESeq2::summary.DESeqResults(res_DESeq2))' * at line 176 found ' cat(DESeq2::DESeqResults(res_DESeq2))'
- In file R/PAC_filter.R: * at line 132 found ' cat(paste0("\n-- Pheno target was specified, will retain: ", ' * at line 177 found ' cat(paste0("\n-- Anno target was specified, will retain: ", ' * at line 205 found ' cat(paste0("\n-- Size filter will retain: ", ' * at line 218 found ' cat("\n-- Count filter was specified.")' * at line 221 found ' cat(paste0("\n-- Filter on normalized (", ' * at line 286 found ' cat("\n!! !!\nUser input needed:\n") ' * at line 298 found ' cat(paste0("\n-- The chosen filters will retain: ", '
- In file R/PAC_gtf.R: * at line 268 found ' cat("\nImporting gtf files ...")' * at line 318 found ' cat("\nNo genome fasta was found, will atempt", ' * at line 325 found ' cat("\nInput genome was an existing file. Will treat it as a",' * at line 397 found ' cat("\n\nReorganizing coordinates ...")' * at line 422 found ' cat("\n\nChromosome names compatibility check ...")' * at line 438 found ' cat("\n")' * at line 449 found ' cat("\n")' * at line 450 found ' cat(' * at line 460 found ' cat("\n\nAnnotating against the gtf file(s) ...")' * at line 511 found ' cat(paste0("\n |--> Extract and compile '", gtf_nam, "' ...")) ' * at line 554 found ' cat("\n\n")' * at line 558 found ' cat("\rGenerating full annotation list: ", i, "/", loop)' * at line 570 found ' cat("\n\n")' * at line 574 found ' cat("\rGenerating simplified annotation table: ", i, "/", loop)'
- In file R/PAC_mapper.R: * at line 225 found ' cat("\nImporting reference from DNAStringSet ...")' * at line 229 found ' cat("\nReading reference from fasta file ...")' * at line 233 found ' cat("\nTry to import reference from character vector ...")' * at line 272 found ' cat("\nBowtie indexes found. Will try to use them...")' * at line 277 found ' cat("\nNo bowtie indexes.")' * at line 278 found ' cat("\nWill try to reindex references ...")'
- In file R/PAC_nbias.R: * at line 149 found ' cat(paste0("\nCounting nucleotides"))'
- In file R/PAC_saturation.R: * at line 70 found ' cat("\nOrganizing data...\n") ' * at line 78 found ' cat(paste0("\nPermutations will be generated using ", threads, " of ", parallel::detectCores(), " available core workers.")) ' * at line 79 found ' cat(paste0("\nMaking ", resample, " permutations at ", steps," equally distributed sequence depths."))' * at line 80 found ' cat(paste0("\nData will be saved for two coverage thresholds at >= ", thresh[1], " counts and >= ", thresh[2], " counts\n")) ' * at line 114 found ' cat("\nNow fitting the Asymptotic curve and plotting the results...\n")'
- In file R/PAC_trna.R: * at line 416 found ' return(cat("\nPaired samples are not yet implemented in the function,",'
- In file R/seqpac_generics_methods.R: * at line 366 found ' cat("PAC object with: \n")' * at line 367 found ' cat(" ", nrow(pac$Pheno), "samples\n")' * at line 368 found ' cat(" ",nrow(pac$Anno), "sequences\n")' * at line 374 found ' cat(paste0(" mean total counts: ", avg, " (min:", mn, "/max:", mx, ")\n"))' * at line 375 found ' cat(" best sequence:", mx_seq, "mean counts\n")' * at line 376 found ' cat(" worst sequence:", mn_seq, "mean counts\n")' * at line 378 found ' cat("normalized tables:", length(pac$norm),"\n")' * at line 379 found ' cat(names(pac$norm),"\n")' * at line 382 found ' cat("summarized tables:", length(pac$summary),"\n")' * at line 383 found ' cat(names(pac$summary),"\n")'
- In file R/seqpac_S4classes.R: * at line 356 found ' return(cat("\nSequence names are not identical.",' * at line 361 found ' @.***_anno is not a tibble.",'
- In file R/simplify_reanno.R: * at line 328 found ' cat(paste0("\nNumber of mismatches specified by user: ", ' * at line 351 found ' cat(paste0("\nBiotypes will be asigned as follows:\n"))'
- In file R/tRNA_class.R: * at line 156 found ' cat("The map object contains references without hits.",'
- [ ] No paste in message(), warning, stop
- In file R/make_cutadapt.R: * at line 165 found ' stop(paste0('
- In file R/make_reanno.R: * at line 256 found ' warning(paste( "Missing references in Reanno file(s):\n", ' * at line 321 found ' stop(paste0(' * at line 343 found ' warning(paste0(" Not all missing annotations were found in ", '
- In file R/make_trim.R: * at line 278 found ' stop(paste0("\n There are files in the output folder:\n ", '
- In file R/map_reanno.R: * at line 293 found ' warning(paste0("\n There are files in the output folder:\n ", ' * at line 299 found ' warning(paste0("\n There are files in the output folder:\n ", ' * at line 305 found ' stop(paste0("Please move or delete the files in the output folder."))'
- In file R/PAC_check.R: * at line 58 found ' stop(paste0("\nSample names in Pheno (row names) and Counts",' * at line 62 found ' stop(paste0("\nSequence names in Anno (row names) and Counts",' * at line 98 found ' stop(paste0("\nSample (row) names in new table are not identical",' * at line 104 found ' stop(paste0("\nSample (column) names in new table are not identical",' * at line 120 found ' stop(paste0(' * at line 129 found ' stop(paste0(' * at line 192 found ' stop(paste0('
- In file R/PAC_summary.R: * at line 107 found ' stop(paste0("\nThere is no object called '", norm, "' in the norm list.",'
- [ ] :: is not suggested in source code unless you can make sure all the packages are imported.
- [ ] 1:n is not suggested in source code. Use seq_along or seq.int instead.
- In file R/add_reanno.R: * at line 246 found ' for (i in 1:(mismatches+1)){' * at line 251 found ' for (a in 1:length(full_lst)){' * at line 301 found ' for(z in 1:length(fin_lst)){' * at line 318 found ' for (i in 1:(mismatches+1)){' * at line 324 found ' for (a in 1:length(bio_search)){' * at line 445 found ' colsrch <- c("Mis0_bio", paste0("Mis0_bio", 1:100))' * at line 449 found ' colsrch <- c("Mis0_genome", paste0("Mis0_genome", 1:100))'
- In file R/filtsep_bin.R: * at line 70 found ' for(i in 1:length(filtsep_lst)){'
- In file R/import_reanno.R: * at line 107 found ' for (k in 1:length(files)){' * at line 171 found ' bowtie_out_lst[[k]] <- foreach::foreach(s=1:length(chnks_rng[[1]]), '
- In file R/make_conv.R: * at line 154 found ' for(i in 1:length(ref1_md5_vec)){' * at line 189 found ' for(i in 1:length(ref1_md5_vec)){' * at line 226 found ' for(i in 1:length(hits1)){' * at line 290 found ' for(i in 1:length(reference_list)){' * at line 292 found ' colnames(df)[1:length(reference_list)]))'
- In file R/make_counts.R: * at line 401 found ' seq_lst <- foreach::foreach(i=1:length(fls), .final = function(x){' * at line 487 found ' reads_lst <- foreach::foreach(i=1:length(fls),.final = function(x){' * at line 552 found ' stat_dt$sample <- paste0("fastq_", 1:length(stat_dt$sample))'
- In file R/make_cutadapt.R: * at line 178 found ' prog_report <- foreach::foreach(i=1:length(fls), '
- In file R/make_pheno.R: * at line 207 found ' for(i in 1:nrow(df)){' * at line 214 found ' for(i in 1:nrow(df)){'
- In file R/make_reanno.R: * at line 209 found ' seqs <- (seq(1:length(files)))-1' * at line 211 found ' for(i in 1:length(files)){' * at line 263 found ' for(j in 1:length(NA_which)){' * at line 268 found ' for(g in 1:length(NA_which[[j]])){' * at line 295 found ' for (bio in 1:bio_cat){'
- In file R/make_trim.R: * at line 248 found ' decreasing = TRUE)[1:par_ns])/1000000000' * at line 305 found ' i=1:length(fls), .inorder = TRUE, .export= c("nam_trim", "nam"),' * at line 414 found ' for(z in 1:length(start_gone)){' * at line 623 found ' names(enc))[paste0(enc) %in% as.character(1:quality["threshold"]-1)]' * at line 653 found ' for(i in 1:length(prog_report)){' * at line 666 found ' for(i in 1:length(prog_report)){'
- In file R/map_rangetype.R: * at line 193 found ' intervals=list(start=1:5, mid=45:55, end=95:100), ' * at line 216 found ' for(i in 1:length(map)){' * at line 289 found ' for (i in 1:length(logi_breaks)){' * at line 376 found ' for(i in 1:nrow(fin_ss_df)){' * at line 441 found ' for (k in 1:nrow(code_split)){' * at line 447 found ' for (k in 1:nrow(code_split)){'
- In file R/map_reanno.R: * at line 342 found ' for(i in 1:length(mis_lst)){' * at line 349 found ' for (j in 1:length(ref_paths)){'
- In file R/merge_lanes.R: * at line 142 found ' done <- foreach::foreach(j=1:length(fls_nam)) %dopar% {' * at line 149 found ' for(i in 1:length(lns)){'
- In file R/PAC_check.R: * at line 116 found ' if(sum(grepl(paste(rownames(PAC$Pheno)[1:2], collapse="|"), ' * at line 125 found ' if(sum(grepl(paste(rownames(PAC$Pheno)[1:2], collapse="|"), '
- In file R/PAC_covplot.R: * at line 232 found ' for(i in 1:length(multi_seq_lst)){' * at line 251 found ' for(i in 1:length(ref_data_lst)){' * at line 275 found ' for(i in 1:length(sub_map)){' * at line 281 found ' cov_lst[[i]] <- lapply(as.list(1:length(summary_target[[2]])), function(x){' * at line 285 found ' Position=as.factor(1:IRanges::width(sub_map[[i]]$Ref_seq)), ' * at line 293 found ' fin <- data.frame(Position=ordered(as.factor(1:length(cov))), ' * at line 314 found ' for(i in 1:length(cov_lst)){'
- In file R/PAC_deseq.R: * at line 133 found ' for (i in 1:length(cols)){'
- In file R/PAC_filter.R: * at line 252 found ' for (i in 1:length(filt_plot$x_graph)){ '
- In file R/PAC_gtf.R: * at line 265 found ' names(gtf) <- 1:length(gtf)' * at line 283 found ' for (i in 1:length(gtf_lst)){' * at line 402 found ' for(i in 1:nrow(mis_genome)){' * at line 427 found ' for(i in 1:length(gtf_lst)){' * at line 478 found ' coord_gr <- foreach::foreach(i=1:length(coord_lst), ' * at line 509 found ' for(i in 1:length(gtf_gr)){' * at line 515 found ' coord_anno <- foreach::foreach(t=1:length(coord_gr), ' * at line 557 found ' for(i in 1:loop){' * at line 561 found ' for(z in 1:length(anno_lst)){' * at line 573 found ' for(i in 1:loop){' * at line 577 found ' for(z in 1:length(anno_lst)){'
- In file R/PAC_jitter.R: * at line 167 found ' plt_lst <- as.list(1:ncol(df))'
- In file R/PAC_mapper.R: * at line 309 found ' for(i in 1:length(align_lst)){' * at line 369 found ' for(i in 1:length(align_lst)){' * at line 407 found ' positions_lst <- foreach::foreach(j=1:length(algn_lst), '
- In file R/PAC_nbias.R: * at line 184 found ' for(i in 1:length(nuc_lst)){'
- In file R/PAC_norm.R: * at line 61 found ' for (i in 1:length(lib_sizes)){'
- In file R/PAC_pca.R: * at line 124 found ' colnames(data) <- paste(labels, 1:ncol(data), sep="_")'
- In file R/PAC_pie.R: * at line 166 found ' for(i in 1:length(x)){' * at line 180 found ' for (i in 1:length(tot_cnts)){ ' * at line 192 found ' bio <- bio[c(extra, (1:length(bio))[!1:length(bio) %in% extra])] '
- In file R/PAC_saturation.R: * at line 81 found ' resampl_sub_lst <- foreach::foreach(i=1:length(x_vect), .inorder=FALSE) %dopar% {' * at line 95 found ' for(t in 1:length(thresh)){' * at line 159 found ' names(plots) <- paste("thresh", 1:length(thresh), sep="_")'
- In file R/PAC_sizedist.R: * at line 173 found ' for(i in 1:length(anno_target[[2]])){ ' * at line 196 found ' for(i in 1:length(size_lst)){'
- In file R/PAC_stackbar.R: * at line 152 found ' for(i in 1:length(x)){' * at line 166 found ' for (i in 1:length(tot_cnts)){ '
- In file R/PAC_summary.R: * at line 144 found ' combn_lst <- as.list(data.frame(utils::combn(1:length(sub_data_lst),m = 2)))'
- In file R/PAC_trna.R: * at line 312 found ' df <- df[rep( 1:length(missing), times=length(unique(y$variable))),]' * at line 332 found ' ordr <- ordr[1:top] # Extract the top '
- In file R/simplify_reanno.R: * at line 301 found ' if(sum(names(input)[1:3] == c("Pheno", "Anno", "Counts"))==3){' * at line 363 found ' Hierarchy=1:(nrow(catg)), ' * at line 381 found ' for(i in 1:length(search_terms)){'
- [ ] Vectorize: no unnecessary for loops present.
- In file R/add_reanno.R: * at line 246 found ' for (i in 1:(mismatches+1)){' * at line 251 found ' for (a in 1:length(full_lst)){' * at line 301 found ' for(z in 1:length(fin_lst)){' * at line 318 found ' for (i in 1:(mismatches+1)){' * at line 324 found ' for (a in 1:length(bio_search)){'
- In file R/filtsep_bin.R: * at line 70 found ' for(i in 1:length(filtsep_lst)){'
- In file R/import_reanno.R: * at line 107 found ' for (k in 1:length(files)){'
- In file R/make_conv.R: * at line 154 found ' for(i in 1:length(ref1_md5_vec)){' * at line 189 found ' for(i in 1:length(ref1_md5_vec)){' * at line 226 found ' for(i in 1:length(hits1)){' * at line 290 found ' for(i in 1:length(reference_list)){'
- In file R/make_pheno.R: * at line 207 found ' for(i in 1:nrow(df)){' * at line 214 found ' for(i in 1:nrow(df)){'
- In file R/make_reanno.R: * at line 211 found ' for(i in 1:length(files)){' * at line 263 found ' for(j in 1:length(NA_which)){' * at line 268 found ' for(g in 1:length(NA_which[[j]])){' * at line 295 found ' for (bio in 1:bio_cat){'
- In file R/make_trim.R: * at line 414 found ' for(z in 1:length(start_gone)){' * at line 653 found ' for(i in 1:length(prog_report)){' * at line 666 found ' for(i in 1:length(prog_report)){'
- In file R/map_rangetype.R: * at line 216 found ' for(i in 1:length(map)){' * at line 289 found ' for (i in 1:length(logi_breaks)){' * at line 376 found ' for(i in 1:nrow(fin_ss_df)){' * at line 441 found ' for (k in 1:nrow(code_split)){' * at line 447 found ' for (k in 1:nrow(code_split)){'
- In file R/map_reanno.R: * at line 342 found ' for(i in 1:length(mis_lst)){' * at line 349 found ' for (j in 1:length(ref_paths)){'
- In file R/merge_lanes.R: * at line 149 found ' for(i in 1:length(lns)){'
- In file R/PAC_covplot.R: * at line 232 found ' for(i in 1:length(multi_seq_lst)){' * at line 251 found ' for(i in 1:length(ref_data_lst)){' * at line 275 found ' for(i in 1:length(sub_map)){' * at line 314 found ' for(i in 1:length(cov_lst)){'
- In file R/PAC_deseq.R: * at line 133 found ' for (i in 1:length(cols)){'
- In file R/PAC_filter.R: * at line 252 found ' for (i in 1:length(filt_plot$x_graph)){ '
- In file R/PAC_gtf.R: * at line 283 found ' for (i in 1:length(gtf_lst)){' * at line 402 found ' for(i in 1:nrow(mis_genome)){' * at line 427 found ' for(i in 1:length(gtf_lst)){' * at line 509 found ' for(i in 1:length(gtf_gr)){' * at line 557 found ' for(i in 1:loop){' * at line 561 found ' for(z in 1:length(anno_lst)){' * at line 573 found ' for(i in 1:loop){' * at line 577 found ' for(z in 1:length(anno_lst)){'
- In file R/PAC_mapper.R: * at line 309 found ' for(i in 1:length(align_lst)){' * at line 369 found ' for(i in 1:length(align_lst)){'
- In file R/PAC_nbias.R: * at line 184 found ' for(i in 1:length(nuc_lst)){'
- In file R/PAC_norm.R: * at line 61 found ' for (i in 1:length(lib_sizes)){'
- In file R/PAC_pie.R: * at line 166 found ' for(i in 1:length(x)){' * at line 180 found ' for (i in 1:length(tot_cnts)){ '
- In file R/PAC_saturation.R: * at line 95 found ' for(t in 1:length(thresh)){'
- In file R/PAC_sizedist.R: * at line 173 found ' for(i in 1:length(anno_target[[2]])){ ' * at line 196 found ' for(i in 1:length(size_lst)){'
- In file R/PAC_stackbar.R: * at line 152 found ' for(i in 1:length(x)){' * at line 166 found ' for (i in 1:length(tot_cnts)){ '
- In file R/simplify_reanno.R: * at line 381 found ' for(i in 1:length(search_terms)){'
- [ ] Use file.path to replace paste
- In file R/make_counts.R: * at line 250 found ' output <- paste0(tempdir(), "/seqpac/")'
- In file R/map_reanno.R: * at line 317 found ' filepath=paste0(output_path, "/anno_mis0.fa"), ' * at line 347 found ' input_file <- paste0(output_path, "/anno_mis", mis_lst[[i]], ".fa")' * at line 401 found ' save(reanno, file= paste0(output_path, "/Full_reanno_", suffix, ".Rdata"))'
- In file R/merge_lanes.R: * at line 145 found ' out_nam <- paste0(out_path, "/", fl_base, ".fastq.gz")'
- In file R/PAC_mapper.R: * at line 248 found ' outpath <- paste0(tempdir(), "/", "seqpac")' * at line 249 found ' ref_path <- paste0(tempdir(), "/ref/reference.fa")'
- [ ] Avoid redundant 'stop' and 'warn*' in signal conditions. Found in files:
R/PAC_filter.R (line 114, column 11)
R/PAC_filter.R (line 227, column 12)
R/PAC_filter.R (line 230, column 12)
R/PAC_gtf.R (line 389, column 5)
- [ ] Avoid 'suppressWarnings'/'*Messages' if possible (found 13 times)
in R/make_conv.R (line 293, column 7)
in R/make_counts.R (line 253, column 7)
in R/make_cutadapt.R (line 153, column 5)
in R/make_trim.R (line 285, column 5)
in R/map_reanno.R (line 309, column 5)
in R/PAC_filter.R (line 259, column 7)
in R/PAC_gtf.R (line 370, column 13)
in R/PAC_gtf.R (line 527, column 17)
in R/PAC_mapper.R (line 253, column 3)
in R/PAC_mapper.R (line 257, column 3)
in R/PAC_pca.R (line 105, column 12)
in R/PAC_pca.R (line 109, column 12)
in R/PAC_trna.R (line 466, column 9)
- [ ] Function arguments are tested for validity.
- [ ] Functional programming: code repetition. eg repetition in colnames and rownames

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Feb 01 '22 18:02 Danis102

Received a valid push on git.bioconductor.org; starting a build for commit id: 0138aa29d65f0b5597adfb6067879d87dae7ec89

Feb 02 '22 18:02 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, ERROR, TIMEOUT". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

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Feb 02 '22 18:02 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: e11a97c319d683aaa2b181e34c4e4b77d31754a8

Feb 03 '22 14:02 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "TIMEOUT, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Feb 03 '22 14:02 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: b7bd08723373ea2bdf4f29cefd591d78e5872b2a

Feb 03 '22 18:02 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "TIMEOUT". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Feb 03 '22 18:02 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: b47647cd087bf1105cdb9010f41be19ec2033ff7

Feb 04 '22 08:02 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "TIMEOUT". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Feb 04 '22 09:02 bioc-issue-bot

Dear Bioconductor reviewer,

We consistently recieve a Timeout error on the Mac server when making a new push. All other platforms go through without a problem. In the last push I even removed the two most time consuming test files, saving about 10 min in processing time, and still Mac report timeout error. Please indicate if you are having problems with the Mac server, or give me more specific information of what is wrong with our package on your Mac system.

Best regards, Daniel Natt

Skaffa Outlook för Androidhttps://aka.ms/ghei36

From: bioc-issue-bot @.> Sent: Friday, February 4, 2022 10:21:22 AM To: Bioconductor/Contributions @.> Cc: Daniel Nätt @.>; Mention @.> Subject: Re: [Bioconductor/Contributions] Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation (#2275)

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "TIMEOUT". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build reporthttps://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2Fspb_reports%2Fseqpac_buildreport_20220204042108.html&data=04%7C01%7Cdaniel.natt%40liu.se%7Ce8640289a7ca4d57f68608d9e7bfb672%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637795632849862904%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=ELqSB2iyCQI2N60FCcKHmIP2tGF5Ozyur5XLgTJ6WQQ%3D&reserved=0 for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to @.***:packages/seqpac to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found herehttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fnew-package-workflow%2F&data=04%7C01%7Cdaniel.natt%40liu.se%7Ce8640289a7ca4d57f68608d9e7bfb672%7C913f18ec7f264c5fa816784fe9a58edd%7C0%7C0%7C637795632849862904%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=1rUSbBe5SlT4iMiBl5cJX1z5gVbsnHbO50YcwqN3tnQ%3D&reserved=0.

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Feb 04 '22 13:02 Danis102

There are several functions that are taking a long time on mac. Here is the seqpack-Ex.timings from our build system for merida1

merida1:seqpac.Rcheck pkgbuild$ cat seqpac-Ex.timings 
name	user	system	elapsed
PAC	0.238	0.009	0.324	
PAC_check	0.190	0.006	0.214	
PAC_covplot	51.285	 1.012	57.015	
PAC_deseq	90.392	15.140	74.728	
PAC_filter	0.265	0.009	0.280	
PAC_filtsep	0.229	0.004	0.238	
PAC_gtf	72.651	 4.932	46.092	
PAC_jitter	14.018	 0.320	16.245	
PAC_mapper	49.646	 0.846	55.971	
PAC_nbias	16.611	 0.078	17.887	
PAC_norm	4.185	0.012	4.527	
PAC_pca	17.151	 0.173	18.314	
PAC_pie	2.995	0.060	3.215	
PAC_saturation	2.520	0.035	2.676	
PAC_sizedist	4.153	0.037	4.430	
PAC_stackbar	3.907	0.077	4.168	
PAC_summary	1.782	0.006	1.859	
PAC_trna	17.937	 4.818	22.961	
add_reanno	30.307	 5.192	36.910	
anno	0.338	0.106	0.446	
as.PAC	0.220	0.004	0.225	
as.reanno	19.634	 3.870	20.581	
colnames	0.342	0.109	0.455	
counts	0.339	0.110	0.455	
filtsep_bin	0.224	0.005	0.229	
full	15.302	 3.758	16.071	
import_reanno	5.969	1.310	6.955	
length	0.348	0.111	0.462	
make_PAC	42.762	 7.338	37.543	
make_conv	0.102	0.004	0.116	
make_counts	79.870	15.191	76.648	
make_cutadapt	32.971	 0.881	36.983	
make_pheno	39.205	 9.452	34.955	
make_reanno	10.030	 2.295	10.484	
make_trim	34.092	 0.714	34.920	
map_rangetype	 7.771	 3.718	11.283	
map_reanno	66.331	13.110	68.910	
merge_lanes	 7.248	 0.725	10.540	
names	15.277	 3.708	17.318	
ncol	0.301	0.097	0.400	
norm	0.298	0.082	0.381	
nrow	0.287	0.103	0.391	
overview	15.905	 3.901	19.317	
pheno	0.344	0.114	0.692	
reanno	20.873	 3.987	26.416	
rownames	0.311	0.101	0.414	
show	0.305	0.095	0.402	
simplify_reanno	22.250	 4.143	33.875	
summary	0.343	0.106	0.691	
tRNA_class	17.561	 4.231	25.132

These functions also take several seconds on the other platforms so perhaps there is a way to look for inefficiencies and ways to improve the timing. For comparison here is the example timings from nebbiolo1

seqpac.Rcheck$ cat seqpac-Ex.timings 
name	user	system	elapsed
PAC	0.075	0.004	0.079	
PAC_check	0.060	0.001	0.060	
PAC_covplot	15.774	 0.433	16.206	
PAC_deseq	26.809	 8.057	22.807	
PAC_filter	0.094	0.000	0.094	
PAC_filtsep	0.076	0.000	0.076	
PAC_gtf	20.109	 2.983	13.620	
PAC_jitter	4.617	0.096	4.713	
PAC_mapper	14.195	 0.451	14.643	
PAC_nbias	4.513	0.024	4.537	
PAC_norm	1.108	0.004	1.112	
PAC_pca	5.263	0.104	5.367	
PAC_pie	0.823	0.040	0.863	
PAC_saturation	0.758	0.017	0.793	
PAC_sizedist	1.162	0.012	1.174	
PAC_stackbar	1.111	0.008	1.119	
PAC_summary	0.425	0.000	0.425	
PAC_trna	5.547	5.245	7.466	
add_reanno	11.161	 2.742	12.469	
anno	0.099	0.124	0.224	
as.PAC	0.067	0.004	0.071	
as.reanno	7.395	1.984	8.087	
colnames	0.120	0.100	0.219	
counts	0.092	0.128	0.221	
filtsep_bin	0.078	0.004	0.082	
full	6.606	1.973	7.320	
import_reanno	2.930	0.751	3.389	
length	0.109	0.112	0.221	
make_PAC	22.330	 2.661	18.362	
make_conv	0.034	0.000	0.034	
make_counts	42.498	 6.043	35.342	
make_cutadapt	18.616	 0.260	18.876	
make_pheno	21.767	 2.568	17.976	
make_reanno	4.307	1.366	4.823	
make_trim	19.590	 0.296	19.886	
map_rangetype	2.587	5.163	4.414	
map_reanno	24.051	 6.650	23.713	
merge_lanes	2.971	0.385	3.301	
names	7.218	2.245	8.152	
ncol	0.097	0.120	0.218	
norm	0.092	0.124	0.216	
nrow	0.103	0.116	0.219	
overview	6.887	2.120	7.698	
pheno	0.110	0.112	0.223	
reanno	8.138	1.936	8.778	
rownames	0.08	0.14	0.22	
show	0.098	0.132	0.230	
simplify_reanno	8.053	2.120	8.869	
summary	0.094	0.128	0.221	
tRNA_class	5.536	5.368	7.581

Feb 17 '22 13:02 lshep

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Submission of new package, seqpac: for small RNA analysis: from fastq (trimming included) to interpretation

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