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This page was generated on 2024-05-22 11:37:02 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4665
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4400
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4427
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 1273/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mogsa 1.39.0  (landing page)
Chen Meng
Snapshot Date: 2024-05-20 14:05:07 -0400 (Mon, 20 May 2024)
git_url: https://git.bioconductor.org/packages/mogsa
git_branch: devel
git_last_commit: f4d1b5d
git_last_commit_date: 2024-04-30 10:42:59 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows 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 / arm64see weekly results here

CHECK results for mogsa on palomino4


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: 1.39.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mogsa.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mogsa_1.39.0.tar.gz
StartedAt: 2024-05-21 02:42:57 -0400 (Tue, 21 May 2024)
EndedAt: 2024-05-21 02:45:36 -0400 (Tue, 21 May 2024)
EllapsedTime: 159.0 seconds
RetCode: 0
Status:   OK  
CheckDir: mogsa.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mogsa.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mogsa_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/mogsa.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'mogsa/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mogsa' version '1.39.0'
* 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 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/mogsa.Rcheck/00check.log'
for details.


Installation output

mogsa.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL mogsa
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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
GIS0.640.030.68
annotate.gs0.120.000.12
bootMbpca000
bootMoa000
box.gs.feature0.210.020.24
combine-methods0.250.030.28
decompose.gs.group0.530.030.56
decompose.gs.ind0.120.000.13
distMoa0.210.010.21
getmgsa0.120.000.13
matpower000
mbpca2.580.212.78
mgsa-class0.170.030.20
moGap1.390.141.54
moa-class0.080.000.07
moa0.550.050.60
moa.sup-class0.090.000.09
moaCoef0.190.030.22
moaScore0.200.010.22
mogsa-package0.190.020.20
mogsa0.280.000.28
pairwise.rv0.020.000.01
plotGS0.110.000.11
prepGraphite0.280.000.28
prepMsigDB0.010.000.02
prepSupMoa4.360.194.56
softK000
sup.moa0.260.000.26
wsvd000