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ccImpute software package submission
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- Repository: https://github.com/khazum/ccImpute
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Hi @khazum
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: ccImpute
Type: Package
Title: ccImpute: an accurate and scalable consensus clustering based approach to
impute dropout events in the single-cell RNA-seq data
Version: 0.99.0
Authors@R: person("Marcin", "Malec",
email = "[email protected]",
role = c("cre", "aut"),
comment = c(ORCID = "0000-0002-2354-513X"))
Description: Dropout events make the lowly expressed genes indistinguishable
from true zero expression and different than the low expression present in
cells of the same type. This issue makes any subsequent downstream analysis
difficult. ccImpute is an imputation algorithm that uses cell similarity
established by consensus clustering to impute the most probable dropout
events in the scRNA-seq datasets. ccImpute demonstrated performance which
exceeds the performance of existing imputation approaches while introducing
the least amount of new noise as measured by clustering performance
characteristics on datasets with known cell identities.
License: GPL-3
Imports: Rcpp, doParallel, foreach, matrixStats, parallel, stats, SIMLR
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.1.2
biocViews: SingleCell, PrincipalComponent, DimensionReduction,
Clustering, RNASeq, Transcriptomics
biocType: Software
Suggests:
knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater,
SingleCellExperiment, mclust
VignetteBuilder: knitr
on a mac that can install just about anything:
* installing *source* package 'ccImpute' ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/Users/vincentcarey/R-dev-dist/lib/R/include" -DNDEBUG -I'/Users/vincentcarey/R-dev-dist/lib/R/library/Rcpp/include' -I'/Users/vincentcarey/R-dev-dist/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/Users/vincentcarey/R-dev-dist/lib/R/include" -DNDEBUG -I'/Users/vincentcarey/R-dev-dist/lib/R/library/Rcpp/include' -I'/Users/vincentcarey/R-dev-dist/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -c cppFunctions.cpp -o cppFunctions.o
cppFunctions.cpp:4:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
Please be sure you are configuring in a portable way.
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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". 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/ccImpute to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
I believe the warning has to do with the build system rather than my code. I hope the package review will continue smoothly. Please let me know if I can be of any further assistance.
The warning in the macOS builder looks like something that needs to be addressed in your code: https://bioconductor.org/spb_reports/ccImpute_buildreport_20220429124256.html#merida1_check_anchor I'll see if it reproduces on my Mac. Are you able to install and test the package on Mac?
Can confirm that I get the warning when checking the package on my MacBook Pro (Early-2015).
# Trimmed output of running `R CMD check ccImpute_0.99.0.tar.gz`
* checking compiled code ... WARNING
File ‘ccImpute/libs/ccImpute.so’:
Found ‘___assert_rtn’, possibly from ‘assert’ (C)
Object: ‘RcppExports.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.0 tools_4.2.0 fortunes_1.5-4
I'm not sure of the solution, but I think this indicates it's something you will need to fix within ccImpute.
I have researched this issue further, and I made appropriate changes to the source code that should take care of this warning. I believe the issue is addressed now.
Received a valid push on git.bioconductor.org; starting a build for commit id: b2f6a310f2106fcd37d2d0c8bf21df8ba9ba659c
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, skipped". 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/ccImpute to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: fbfe50bddc7097d3f5d34383fa309edc915e1a48
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". 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/ccImpute to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 65f93b013ee29d84c83390c91ea78e571210f240
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". 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/ccImpute to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 917acc2d2462ebd5f6a3f4892d86a655b809054b
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, skipped". 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/ccImpute to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 9f14388a3e1a8ff4860542c9af9f43bb471c25e7
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, skipped". 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/ccImpute to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: cabce0e55796a37a1a894155047d2b6fdda17a38
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". 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/ccImpute to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: b619983fee81984a3b1ff8a547160df608737ac7
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". 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/ccImpute to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 1baead3e10f1c0ceaf9afa193ce44c40fc2d10b8
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". 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/ccImpute to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: b10e0c5992329c097c0f1c40298385a334cf5d19
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: "skipped, 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/ccImpute to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 5f750bcd30cadc061eee218ca72977bc50455315