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This page was generated on 2025-10-16 12:04 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4867
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4655
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4600
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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 812/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.41.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2025-10-15 13:45 -0400 (Wed, 15 Oct 2025)
git_url: https://git.bioconductor.org/packages/genefu
git_branch: devel
git_last_commit: c144019
git_last_commit_date: 2025-04-15 10:07:38 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for genefu on lconway

To the developers/maintainers of the genefu package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genefu.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: genefu
Version: 2.41.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genefu.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genefu_2.41.0.tar.gz
StartedAt: 2025-10-15 22:23:39 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 22:27:08 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 208.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: genefu.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genefu.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genefu_2.41.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/genefu.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genefu’ version ‘2.41.0’
* 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 ‘genefu’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/genefu.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘AIMS’ ‘biomaRt’ ‘iC10’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘mclust:::grid1’ ‘mclust:::grid2’
  See the note in ?`:::` about the use of this operator.
* 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) fuzzy.ttest.Rd:41: Lost braces; missing escapes or markup?
    41 | in w1 and w2 should lay in [0,1] and \verb{0 <= (w1[i] + w2[i]) <= 1} for i in {0,1,...,n} where
       |                                                                                ^
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/genefu.Rcheck/00check.log’
for details.


Installation output

genefu.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL genefu
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘genefu’ ...
** this is package ‘genefu’ version ‘2.41.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
** testing if installed package keeps a record of temporary installation path
* DONE (genefu)

Tests output


Example timings

genefu.Rcheck/genefu-Ex.timings

nameusersystemelapsed
bimod0.2180.0140.236
boxplotplus20.0080.0010.008
claudinLow1.1380.0311.191
compareProtoCor1.2300.0241.270
compute.pairw.cor.meta1.5630.0391.625
compute.proto.cor.meta1.1700.0211.208
cordiff.dep0.1040.0030.108
endoPredict0.1140.0060.121
fuzzy.ttest0.1560.0250.186
gene700.2590.0100.272
gene760.1360.0130.156
geneid.map0.1370.0100.149
genius0.2300.0210.258
ggi0.1090.0070.117
ihc40.1130.0110.131
intrinsic.cluster0.3850.0180.390
intrinsic.cluster.predict0.1870.0090.216
map.datasets1.1410.0231.172
molecular.subtyping2.2120.1232.369
npi0.1020.0070.124
oncotypedx0.1160.0070.130
ovcAngiogenic0.1370.0110.154
ovcCrijns0.1200.0060.149
ovcTCGA0.2200.0080.242
ovcYoshihara0.1300.0070.144
pik3cags0.1050.0070.137
power.cor000
ps.cluster0.3230.0200.428
read.m.file0.0210.0030.059
rename.duplicate0.0010.0010.012
rescale0.2590.0130.302
rorS0.1840.0090.199
setcolclass.df0.0020.0010.002
sig.score0.1340.0080.146
spearmanCI0.0000.0010.001
st.gallen0.0880.0080.129
stab.fs0.2140.0170.536
stab.fs.ranking1.4420.1112.088
strescR0.0010.0000.001
subtype.cluster0.6650.0580.758
subtype.cluster.predict0.2790.0330.559
tamr130.1410.0210.215
tbrm0.0010.0010.001
weighted.meanvar0.0000.0010.001
write.m.file0.0030.0040.010