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This page was generated on 2021-10-20 12:04:42 -0400 (Wed, 20 Oct 2021).

CHECK results for genefu on nebbiolo2

To the developers/maintainers of the genefu package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 719/2072HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.25.1  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-10-19 14:50:04 -0400 (Tue, 19 Oct 2021)
git_url: https://git.bioconductor.org/packages/genefu
git_branch: master
git_last_commit: 8fce049
git_last_commit_date: 2021-05-21 19:08:16 -0400 (Fri, 21 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: genefu
Version: 2.25.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings genefu_2.25.1.tar.gz
StartedAt: 2021-10-19 20:09:12 -0400 (Tue, 19 Oct 2021)
EndedAt: 2021-10-19 20:11:33 -0400 (Tue, 19 Oct 2021)
EllapsedTime: 141.0 seconds
RetCode: 0
Status:   OK  
CheckDir: genefu.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings genefu_2.25.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/genefu.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genefu’ version ‘2.25.1’
* 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 ... OK
* 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 R 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 ... OK
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/genefu.Rcheck/00check.log’
for details.



Installation output

genefu.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL genefu
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘genefu’ ...
** 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 (genefu)

Tests output


Example timings

genefu.Rcheck/genefu-Ex.timings

nameusersystemelapsed
bimod0.2040.0040.208
boxplotplus20.0080.0000.008
claudinLow0.6260.0120.638
compareProtoCor1.4360.0121.447
compute.pairw.cor.meta1.8380.0321.870
compute.proto.cor.meta1.3720.0081.379
cordiff.dep0.1110.0040.115
endoPredict0.1150.0040.119
fuzzy.ttest0.1120.0000.111
gene700.2620.0120.274
gene760.1290.0040.132
geneid.map0.1230.0000.124
genius0.2120.0040.215
ggi0.1180.0000.119
ihc40.0920.0070.100
intrinsic.cluster0.3900.0040.371
intrinsic.cluster.predict0.1620.0000.162
map.datasets1.4200.0121.432
molecular.subtyping2.3490.0402.390
npi0.0990.0000.099
oncotypedx0.110.000.11
ovcAngiogenic0.1330.0040.137
ovcCrijns0.1140.0000.115
ovcTCGA0.2250.0080.233
ovcYoshihara0.1070.0120.119
pik3cags0.1040.0080.112
power.cor000
ps.cluster0.3480.0040.331
read.m.file0.0180.0000.018
rename.duplicate0.0010.0000.001
rescale0.2170.0080.224
rorS0.1640.0040.168
setcolclass.df0.0010.0000.001
sig.score0.1100.0040.114
spearmanCI0.0010.0000.000
st.gallen0.0970.0040.102
stab.fs0.0660.0000.066
stab.fs.ranking0.4560.0080.465
strescR0.0000.0000.001
subtype.cluster0.6550.0240.679
subtype.cluster.predict0.2600.0040.264
tamr130.1250.0080.134
tbrm0.0000.0000.001
weighted.meanvar000
write.m.file0.0040.0000.003