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Published 20 hours ago • verified publisher icon sigven

error running in example code

Open sumin5784 opened this issue 9 months ago • 4 comments

Describe the bug I installed the package and ran the example code in document, and I got this error. I tried with other query gene sets but the error was the same.

INFO  [2025-02-20 13:14:18] WARNING: target gene identifiers NOT found as primary symbols: CCDC101, SMEK1, MGEA5, DGCR14
INFO  [2025-02-20 13:14:18] Trying to map target gene identifiers as gene aliases/synonyms: CCDC101, SMEK1, MGEA5, DGCR14
INFO  [2025-02-20 13:14:18] Mapped query identifiers as gene aliases CCDC101, SMEK1, MGEA5, DGCR14 ---> SGF29, PPP4R3A, OGA, ESS2
INFO  [2025-02-20 13:14:18] SUCCESS: Identified all genes (n = 134) in target set
INFO  [2025-02-20 13:14:18] Open Targets Platform: annotation of protein targets to disease phenotypes (minimum association score =  0.05)
INFO  [2025-02-20 13:14:18] Open Targets Platform: annotation of protein targets to targeted drugs (cancer indications only)
INFO  [2025-02-20 13:14:18] Open Targets Platform: annotation of target tractabilities (druggability)
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA: performing gene enrichment analysis of target set with clusterProfiler
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA clusterProfiler settings: p_value_cutoff = 0.05, q_value_cutoff = 0.2
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA clusterProfiler settings: p_value_adjustment_method = BH
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA clusterProfiler settings: minGSSize = 10
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA clusterProfiler settings: maxGSSize = 500
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA clusterProfiler settings: Background geneset: 'All protein-coding genes'
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA clusterProfiler settings: Background geneset size = 20599
Error in `dplyr::rename()`:
! Can't rename columns that don't exist.
x Column `RichFactor` doesn't exist.
Run `rlang::last_trace()` to see where the error occurred.
  1. The version of oncoEnrichR used: oncoEnrichR_1.5.2
  2. The queryset used (gene identifiers): I ran example code in document
  3. The complete set options (explicitly) set when running oncoEnrichR: I ran example code in document (see below)
library(oncoEnrichR)
myc_interact_targets <- read.csv(system.file("extdata","myc_data.csv", package = "oncoEnrichR"), stringsAsFactors = F)
oeDB <- oncoEnrichR::load_db(cache_dir = "<LOCAL_FOLDER>")
myc_report <- oncoEnrichR::onco_enrich(
  query = myc_interact_targets$symbol, 
  oeDB = oeDB, 
  project_title = "cMYC BioID screen", 
  project_owner = "Raught et al."
  )
oncoEnrichR::write(report = myc_report, oeDB = oeDB, file = "<LOCAL_FOLDER>/myc_report_oncoenrichr.html", format = "html")
oncoEnrichR::write(report = myc_report, oeDB = oeDB, file = "<LOCAL_FOLDER>/myc_report_oncoenrichr.xlsx", format = "excel")

I didn't have this error with galaxy, I don't know why. Could you please check this? I want to R package instead using galaxy.

Thanks, Sumin

sumin5784 avatar Feb 20 '25 18:02 sumin5784

Hi Sumin,

Thanks for reaching out. I am aware of this one, suspect it has to do with the version of clusterProfiler that is being used. Can you check your version of that package and report back?

best, Sigve

sigven avatar Feb 20 '25 21:02 sigven

Hi, Sigve

Thanks for the quick response. I'm afraid but I can't find the clusterProfiler package even though I attached onroEnrichR package.

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] oncoEnrichR_1.5.2

loaded via a namespace (and not attached): [1] circlize_0.4.16 shape_1.4.6.1 GetoptLong_1.0.5 tidyselect_1.2.0 [5] xfun_0.39 purrr_1.0.1 reshape2_1.4.4 colorspace_2.1-0 [9] vctrs_0.6.5 generics_0.1.3 htmltools_0.5.8.1 stats4_4.1.3 [13] yaml_2.3.7 rlang_1.1.5 pillar_1.10.1 glue_1.6.2 [17] BiocGenerics_0.40.0 RColorBrewer_1.1-3 readxl_1.4.2 matrixStats_0.63.0 [21] foreach_1.5.2 lifecycle_1.0.4 plyr_1.8.8 stringr_1.5.1 [25] munsell_0.5.1 gtable_0.3.6 cellranger_1.1.0 GlobalOptions_0.1.2 [29] codetools_0.2-18 evaluate_1.0.3 knitr_1.45 ComplexHeatmap_2.10.0 [33] IRanges_2.28.0 fastmap_1.1.1 doParallel_1.0.17 parallel_4.1.3 [37] Rcpp_1.0.10 scales_1.3.0 writexl_1.4.2 S4Vectors_0.32.4 [41] rjson_0.2.21 ggplot2_3.5.1 png_0.1-8 digest_0.6.31 [45] stringi_1.7.12 dplyr_1.1.4 grid_4.1.3 clue_0.3-64 [49] ggvenn_0.1.10 cli_3.6.1 tools_4.1.3 magrittr_2.0.3 [53] tibble_3.2.1 cluster_2.1.4 crayon_1.5.3 tidyr_1.3.0 [57] pkgconfig_2.0.3 rmarkdown_2.29 rstudioapi_0.17.1 iterators_1.0.14 [61] R6_2.6.0 compiler_4.1.3

So, I tried installing clusterProfiler package manually but there were dependency issues, requiring me to install aplot package, and it induced another error, and so on. I'm using R 4.1.3 now, but I can try with R 4.2 if you want.

Best, Sumin

From: Sigve Nakken @.> Sent: Thursday, February 20, 2025 4:38 PM To: sigven/oncoEnrichR @.> Cc: Jo, Sumin @.>; Author @.> Subject: Re: [sigven/oncoEnrichR] error running in example code (Issue #37)

Hi Sumin,

Thanks for reaching out. I am aware of this one, suspect it has to do with the version of clusterProfiler that is being used. Can you check your version of that package and report back?

best, Sigve

— Reply to this email directly, view it on GitHubhttps://github.com/sigven/oncoEnrichR/issues/37#issuecomment-2672743703, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APSJL2ZKU4ODR7ATRARKK5D2QZDOHAVCNFSM6AAAAABXRN2WPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZSG42DGNZQGM. You are receiving this because you authored the thread.Message ID: @.***>

[sigven]sigven left a comment (sigven/oncoEnrichR#37)https://github.com/sigven/oncoEnrichR/issues/37#issuecomment-2672743703

Hi Sumin,

Thanks for reaching out. I am aware of this one, suspect it has to do with the version of clusterProfiler that is being used. Can you check your version of that package and report back?

best, Sigve

— Reply to this email directly, view it on GitHubhttps://github.com/sigven/oncoEnrichR/issues/37#issuecomment-2672743703, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APSJL2ZKU4ODR7ATRARKK5D2QZDOHAVCNFSM6AAAAABXRN2WPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZSG42DGNZQGM. You are receiving this because you authored the thread.Message ID: @.***>

sumin5784 avatar Feb 20 '25 21:02 sumin5784

Hi, Sumin,

Thanks for the feedback. If you are using RStudio, you should be able to see which version of clusterProfiler that have been installed?

Either way, I would suggest upgrading the R version; and either way truly sorry for the inconvience. I am struggling somewhat to make a given version work stable across different R versions, this is also particularly challenging for oncoEnrichR given the large number of package dependencies. But users have been able to use v5.2 successfully, so I suspect that if you can successfully upgrade your clusterProfiler package, it should be working better.. (time will show:))

PS. Reason that this error is not showing for Galaxy, is that it Galaxy is still running a slightly older version (non-quarto based). The quarto-based version of oncoEnrichR (5.x) is not yet operational within Galaxy.

best, Sigve

sigven avatar Feb 21 '25 20:02 sigven

Hi Sigve,

As you recommended, I updated R 4.1 to R 4.2.3 and installed oncoEnrichR package. However, I still have the same error message, complaining about RichFactor. The Version of clusterProfiler is v4.6.2. Any other options that I can try?

Regards, Sumin

From: Sigve Nakken @.> Sent: Friday, February 21, 2025 3:20 PM To: sigven/oncoEnrichR @.> Cc: Jo, Sumin @.>; Author @.> Subject: Re: [sigven/oncoEnrichR] error running in example code (Issue #37)

Hi, Sumin,

Thanks for the feedback. If you are using RStudio, you should be able to see which version of clusterProfiler that have been installed?

Either way, I would suggest upgrading the R version; and either way truly sorry for the inconvience. I am struggling somewhat to make a given version work stable across different R versions, this is also particularly challenging for oncoEnrichR given the large number of package dependencies. But users have been able to use v5.2 successfully, so I suspect that if you can successfully upgrade your clusterProfiler package, it should be working better.. (time will show:))

PS. Reason that this error is not showing for Galaxy, is that it Galaxy is still running a slightly older version (non-quarto based). The quarto-based version of oncoEnrichR (5.x) is not yet operational within Galaxy.

best, Sigve

— Reply to this email directly, view it on GitHubhttps://github.com/sigven/oncoEnrichR/issues/37#issuecomment-2675466107, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APSJL23UF4QEX2T7UB675KL2Q6DBZAVCNFSM6AAAAABXRN2WPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZVGQ3DMMJQG4. You are receiving this because you authored the thread.Message ID: @.***>

[sigven]sigven left a comment (sigven/oncoEnrichR#37)https://github.com/sigven/oncoEnrichR/issues/37#issuecomment-2675466107

Hi, Sumin,

Thanks for the feedback. If you are using RStudio, you should be able to see which version of clusterProfiler that have been installed?

Either way, I would suggest upgrading the R version; and either way truly sorry for the inconvience. I am struggling somewhat to make a given version work stable across different R versions, this is also particularly challenging for oncoEnrichR given the large number of package dependencies. But users have been able to use v5.2 successfully, so I suspect that if you can successfully upgrade your clusterProfiler package, it should be working better.. (time will show:))

PS. Reason that this error is not showing for Galaxy, is that it Galaxy is still running a slightly older version (non-quarto based). The quarto-based version of oncoEnrichR (5.x) is not yet operational within Galaxy.

best, Sigve

— Reply to this email directly, view it on GitHubhttps://github.com/sigven/oncoEnrichR/issues/37#issuecomment-2675466107, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APSJL23UF4QEX2T7UB675KL2Q6DBZAVCNFSM6AAAAABXRN2WPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNZVGQ3DMMJQG4. You are receiving this because you authored the thread.Message ID: @.***>

sumin5784 avatar Feb 21 '25 20:02 sumin5784

Hi Sumin,

Perhaps upgrade clusterProfiler to it's latest version? I will try to bump a new version soon that you can test also.

best, Sigve

sigven avatar Feb 26 '25 13:02 sigven

Btw: which version of DOSE are you running? I think you need at least 3.31 - See https://github.com/YuLab-SMU/DOSE/blob/devel/NEWS.md#dose-3312. Did you manage to upgrade your ClusterProfiler version ? Moving forward, I will require a ClusterProfiler version > 4.13 as package requirement in the DESCRIPTION file for oncoEnrichR.

sigven avatar Feb 27 '25 16:02 sigven

Try new release, that should work, I think. Closing for now.

sigven avatar Feb 27 '25 21:02 sigven

Hi Sigven,

I installed new release but got this error, is it the same clusterProfiler issue?:

Error in dplyr::rename(): ! Can't rename columns that don't exist. ✖ Column zScore doesn't exist. Run rlang::last_trace() to see where the error occurred.

I used R version and these are clusterProfiler and oncoEnrichR versions: [clusterProfiler_4.6.2 oncoEnrichR_1.5.3

From: Sigve Nakken @.> Sent: Thursday, February 27, 2025 4:42 PM To: sigven/oncoEnrichR @.> Cc: Jo, Sumin @.>; Author @.> Subject: Re: [sigven/oncoEnrichR] error running in example code (Issue #37)

Try new release, that should work, I think. Closing for now.

— Reply to this email directly, view it on GitHubhttps://github.com/sigven/oncoEnrichR/issues/37#issuecomment-2689174346, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APSJL25HTNUX4U2RJK3IDYT2R6BEVAVCNFSM6AAAAABXRN2WPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOBZGE3TIMZUGY. You are receiving this because you authored the thread.Message ID: @.***>

[sigven]sigven left a comment (sigven/oncoEnrichR#37)https://github.com/sigven/oncoEnrichR/issues/37#issuecomment-2689174346

Try new release, that should work, I think. Closing for now.

— Reply to this email directly, view it on GitHubhttps://github.com/sigven/oncoEnrichR/issues/37#issuecomment-2689174346, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APSJL25HTNUX4U2RJK3IDYT2R6BEVAVCNFSM6AAAAABXRN2WPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOBZGE3TIMZUGY. You are receiving this because you authored the thread.Message ID: @.***>

sumin5784 avatar Mar 01 '25 20:03 sumin5784

Hi Sumin, Yeah you need to upgrade ClusterProfiler. Your version 4.6.2 is too old version for oncoEnrichR to work properly. I've tried to set this as a requiment in the DESCRIPTION file (clusterProfiler > v4.13), but apparently that's not sufficient to make it install the correct versions. I would actually recommend that you upgrade your BioConductor version (https://bioconductor.org/install/), you're probably having an older version running?

best, Sigve

sigven avatar Mar 01 '25 21:03 sigven