Laurent Gatto
| Snapshot Date: 2023-10-12 07:30:02 -0400 (Thu, 12 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/depmap |
| git_branch: RELEASE_3_17 |
| git_last_commit: b9ee849 |
| git_last_commit_date: 2023-04-25 10:47:25 -0400 (Tue, 25 Apr 2023) |
| Back to Build/check report for BioC 3.17 experimental data |
|
This page was generated on 2023-10-12 14:51:35 -0400 (Thu, 12 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 90/421 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| depmap 1.14.0 (landing page) Laurent Gatto
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | |||||||
|
To the developers/maintainers of the depmap package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: depmap |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:depmap.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings depmap_1.14.0.tar.gz |
| StartedAt: 2023-10-12 11:12:32 -0400 (Thu, 12 Oct 2023) |
| EndedAt: 2023-10-12 11:29:10 -0400 (Thu, 12 Oct 2023) |
| EllapsedTime: 998.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: depmap.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:depmap.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings depmap_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/depmap.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘depmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘depmap’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘depmap’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
checkRd: (7) RPPA.Rd:21: Invalid URL: "https://depmap.org/portal/download/"
checkRd: (7) RPPA.Rd:91: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/28753430"
checkRd: (7) RPPA.Rd:97: Invalid URL: "https://www.nature.com/articles/s41586-019-1186-3"
checkRd: (7) RPPA.Rd:102: Invalid URL: "https://www.nature.com/articles/s41591-019-0404-8"
checkRd: (7) TPM.Rd:34: Invalid URL: "https://depmap.org/portal/download/"
checkRd: (7) TPM.Rd:110: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/28753430"
checkRd: (7) TPM.Rd:113: Invalid URL: "https://figshare.com/articles/DepMap_Achilles_19Q1_Public/7655150"
checkRd: (7) TPM.Rd:120: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/29083409"
checkRd: (7) TPM.Rd:126: Invalid URL: "https://www.nature.com/articles/s41586-019-1186-3"
checkRd: (7) achilles.Rd:26: Invalid URL: "https://depmap.org/portal/download/"
checkRd: (7) achilles.Rd:58: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/28753430"
checkRd: (7) achilles.Rd:66: Invalid URL: "https://www.nature.com/articles/s41467-018-06916-5"
checkRd: (7) copyNumber.Rd:36: Invalid URL: "https://depmap.org/portal/download/"
checkRd: (7) copyNumber.Rd:109: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/28753430"
checkRd: (7) copyNumber.Rd:112: Invalid URL: "https://figshare.com/articles/DepMap_Achilles_19Q1_Public/7655150"
checkRd: (7) copyNumber.Rd:119: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/29083409"
checkRd: (7) copyNumber.Rd:125: Invalid URL: "https://www.nature.com/articles/s41586-019-1186-3"
checkRd: (7) crispr.Rd:34-35: Invalid URL: "https://ndownloader.figshare.com/files/14221385"
checkRd: (7) crispr.Rd:111: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/28753430"
checkRd: (7) crispr.Rd:114: Invalid URL: "https://figshare.com/articles/DepMap_Achilles_19Q1_Public/7655150"
checkRd: (7) crispr.Rd:121: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/29083409"
checkRd: (7) crispr.Rd:127: Invalid URL: "https://www.nature.com/articles/s41586-019-1186-3"
checkRd: (7) drug_sensitivity.Rd:31: Invalid URL: "https://depmap.org/portal/download/"
checkRd: (7) drug_sensitivity.Rd:101: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/28753430"
checkRd: (7) drug_sensitivity.Rd:112: Invalid URL: "https://www.biorxiv.org/content/10.1101/730119v1"
checkRd: (7) gene_summary.Rd:23: Invalid URL: "https://depmap.org/portal/download/"
checkRd: (7) gene_summary.Rd:57: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/28753430"
checkRd: (7) gene_summary.Rd:65: Invalid URL: "https://www.nature.com/articles/s41467-018-06916-5"
checkRd: (7) metadata.Rd:57: Invalid URL: "https://depmap.org/portal/download/"
checkRd: (7) metadata.Rd:141: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/28753430"
checkRd: (7) metadata.Rd:144: Invalid URL: "https://figshare.com/articles/DepMap_Achilles_19Q1_Public/7655150"
checkRd: (7) metadata.Rd:151: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/29083409"
checkRd: (7) metadata.Rd:157: Invalid URL: "https://www.nature.com/articles/s41586-019-1186-3"
checkRd: (7) mutationCalls.Rd:62: Invalid URL: "https://depmap.org/portal/download/"
checkRd: (7) mutationCalls.Rd:138: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/28753430"
checkRd: (7) mutationCalls.Rd:141: Invalid URL: "https://figshare.com/articles/DepMap_Achilles_19Q1_Public/7655150"
checkRd: (7) mutationCalls.Rd:148: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/29083409"
checkRd: (7) mutationCalls.Rd:154: Invalid URL: "https://www.nature.com/articles/s41586-019-1186-3"
checkRd: (7) proteomic.Rd:27: Invalid URL: "https://depmap.org/portal/download/"
checkRd: (7) proteomic.Rd:89: Invalid URL: "https://doi.org/10.1016/j.cell.2019.12.023"
checkRd: (7) rnai.Rd:23: Invalid URL: "https://depmap.org/portal/download/"
checkRd: (7) rnai.Rd:80: Invalid URL: "https://www.ncbi.nlm.nih.gov/pubmed/28753430"
checkRd: (7) rnai.Rd:88: Invalid URL: "https://www.nature.com/articles/s41467-018-06916-5"
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘depmap.Rmd’ using ‘UTF-8’... OK
‘using_depmap.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/home/biocbuild/bbs-3.17-data-experiment/meat/depmap.Rcheck/00check.log’
for details.
depmap.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL depmap ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘depmap’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (depmap)
depmap.Rcheck/depmap-Ex.timings
| name | user | system | elapsed | |
| RPPA | 0.000 | 0.000 | 0.001 | |
| TPM | 0 | 0 | 0 | |
| achilles | 0 | 0 | 0 | |
| copyNumber | 0 | 0 | 0 | |
| crispr | 0 | 0 | 0 | |
| gene_summary | 0.000 | 0.000 | 0.001 | |
| metadata | 0 | 0 | 0 | |
| mutationCalls | 0.000 | 0.001 | 0.000 | |
| proteomic | 0 | 0 | 0 | |
| rnai | 0 | 0 | 0 | |