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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 1315/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mogsa 1.38.0  (landing page)
Chen Meng
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/mogsa
git_branch: RELEASE_3_19
git_last_commit: f3d45d4
git_last_commit_date: 2024-04-30 10:42:59 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for mogsa on nebbiolo1

To the developers/maintainers of the mogsa package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mogsa.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.

raw results


Summary

Package: mogsa
Version: 1.38.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:mogsa.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings mogsa_1.38.0.tar.gz
StartedAt: 2024-06-20 01:18:23 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 01:22:52 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 268.6 seconds
RetCode: 0
Status:   OK  
CheckDir: mogsa.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:mogsa.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings mogsa_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/mogsa.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘mogsa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mogsa’ version ‘1.38.0’
* 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 ‘mogsa’ 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 code 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 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 ... NOTE
checkRd: (-1) GIS.Rd:57: Lost braces; missing escapes or markup?
    57 |         log2(var(GS_{-i})/var(GS))
       |                     ^
checkRd: (-1) GIS.Rd:59: Lost braces; missing escapes or markup?
    59 |         where GS is the gene set score, and the GS_{-i} is a recalculate of 
       |                                                    ^
checkRd: (-1) GIS.Rd:65: Lost braces; missing escapes or markup?
    65 |         log2(F(GS_{-i})/F(GS))
       |                   ^
checkRd: (-1) NCI60_4array_supdata.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:15-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4array_supdata.Rd:19: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4array_supdata.Rd:23: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4array_supdata.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4array_supdata.Rd:27-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:21: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NCI60_4arrays.Rd:33: Escaped LaTeX specials: \$
checkRd: (-1) NCI60_4arrays.Rd:33-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mgsa-class.Rd:22-24: Lost braces
    22 |                 \item{combine}{\code{signature(x = "mgsa", y = "mgsa")}}{
       |                                                                         ^
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/mogsa.Rcheck/00check.log’
for details.


Installation output

mogsa.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL mogsa
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘mogsa’ ...
** using staged installation
** R
** data
** 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 (mogsa)

Tests output


Example timings

mogsa.Rcheck/mogsa-Ex.timings

nameusersystemelapsed
GIS0.9640.1561.121
annotate.gs0.1220.0000.122
bootMbpca000
bootMoa0.0000.0000.001
box.gs.feature0.9350.0681.003
combine-methods0.1870.0360.223
decompose.gs.group0.1210.0040.125
decompose.gs.ind0.1220.0040.125
distMoa0.3760.0000.475
getmgsa0.1190.0030.123
matpower0.0010.0000.001
mbpca3.1510.2043.564
mgsa-class0.2060.0120.218
moGap2.2060.0522.258
moa-class0.0870.0000.087
moa0.6360.0160.652
moa.sup-class0.0890.0010.088
moaCoef0.240.000.24
moaScore0.2360.0000.236
mogsa-package0.1960.0000.195
mogsa0.7110.0030.715
pairwise.rv0.0110.0010.011
plotGS0.1070.0000.107
prepGraphite0.2800.0070.288
prepMsigDB0.0020.0000.002
prepSupMoa4.2110.1404.352
softK000
sup.moa0.2600.0080.268
wsvd0.0000.0010.001