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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 778/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.37.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/genefu
git_branch: devel
git_last_commit: 83765c0
git_last_commit_date: 2024-04-30 10:24:01 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for genefu on merida1

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: 2.37.0
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_2.37.0.tar.gz
StartedAt: 2024-06-10 03:56:30 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 04:01:36 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 306.2 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_2.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/genefu.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genefu’ version ‘2.37.0’
* 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-3.20-bioc/meat/genefu.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
molecular.subtyping 4.804  0.202   5.862
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘genefu’ ...
** 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
bimod0.3840.0240.448
boxplotplus20.0140.0020.017
claudinLow1.6860.0451.902
compareProtoCor1.6070.0291.781
compute.pairw.cor.meta2.3340.0472.545
compute.proto.cor.meta1.5250.0271.713
cordiff.dep0.1900.0080.220
endoPredict0.1970.0120.227
fuzzy.ttest0.2940.0240.345
gene700.5190.0320.606
gene760.2260.0120.261
geneid.map0.2060.0160.242
genius0.4090.0270.479
ggi0.1990.0110.219
ihc40.1800.0170.215
intrinsic.cluster0.7790.0330.866
intrinsic.cluster.predict0.3630.0160.410
map.datasets1.4760.0331.634
molecular.subtyping4.8040.2025.862
npi0.1740.0160.202
oncotypedx0.2030.0140.226
ovcAngiogenic0.2460.0200.283
ovcCrijns0.2040.0110.239
ovcTCGA0.5030.0140.589
ovcYoshihara0.2020.0110.235
pik3cags0.1950.0120.234
power.cor0.0010.0000.002
ps.cluster0.8340.0280.906
read.m.file0.0420.0050.052
rename.duplicate0.0020.0020.004
rescale0.4060.0160.453
rorS0.3650.0140.409
setcolclass.df0.0030.0010.004
sig.score0.2120.0130.244
spearmanCI0.0010.0010.002
st.gallen0.1770.0130.215
stab.fs0.3050.0210.369
stab.fs.ranking1.8040.1012.063
strescR0.0020.0000.003
subtype.cluster1.1290.0951.359
subtype.cluster.predict0.5030.0320.602
tamr130.2410.0130.288
tbrm0.0010.0010.002
weighted.meanvar0.0010.0010.002
write.m.file0.0050.0050.011