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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 804/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.36.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/genefu
git_branch: RELEASE_3_19
git_last_commit: a82c8f1
git_last_commit_date: 2024-04-30 10:24:01 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for genefu on nebbiolo1

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: 2.36.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings genefu_2.36.0.tar.gz
StartedAt: 2024-06-12 23:22:06 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 23:25:09 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 183.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: genefu.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings genefu_2.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/genefu.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 ‘genefu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genefu’ version ‘2.36.0’
* 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/genefu.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
* 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 ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/genefu.Rcheck/00check.log’
for details.


Installation output

genefu.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
bimod0.1950.0120.208
boxplotplus20.0010.0080.009
claudinLow0.6350.0120.647
compareProtoCor1.2000.0431.243
compute.pairw.cor.meta1.5200.0531.572
compute.proto.cor.meta1.3230.0041.327
cordiff.dep0.1010.0120.114
endoPredict0.1040.0120.116
fuzzy.ttest0.0810.0040.084
gene700.2660.0040.270
gene760.1230.0070.130
geneid.map0.1150.0040.120
genius0.2260.0040.230
ggi0.1170.0000.117
ihc40.0970.0110.108
intrinsic.cluster0.3690.0090.363
intrinsic.cluster.predict0.1680.0000.167
map.datasets1.3160.0551.373
molecular.subtyping2.4050.0762.488
npi0.1040.0040.109
oncotypedx0.1220.0010.123
ovcAngiogenic0.1510.0020.153
ovcCrijns0.1180.0000.118
ovcTCGA0.2170.0080.226
ovcYoshihara0.1170.0080.126
pik3cags0.1230.0000.123
power.cor0.0010.0000.000
ps.cluster0.3600.0080.353
read.m.file0.0170.0040.022
rename.duplicate0.0010.0000.002
rescale0.2400.0080.248
rorS0.1740.0000.173
setcolclass.df0.0000.0020.002
sig.score0.1210.0010.122
spearmanCI0.0010.0000.000
st.gallen0.0960.0120.108
stab.fs0.1020.0160.117
stab.fs.ranking0.5360.0240.561
strescR0.0000.0000.001
subtype.cluster0.6600.0160.676
subtype.cluster.predict0.2970.0080.305
tamr130.1340.0040.138
tbrm0.0010.0000.000
weighted.meanvar0.0010.0000.000
write.m.file0.0000.0030.003