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This page was generated on 2021-10-23 14:05:59 -0400 (Sat, 23 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 723/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.25.1  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 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: 2021-10-22 20:11:40 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 20:14:13 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 152.7 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
bimod0.1980.0050.202
boxplotplus20.0030.0030.007
claudinLow0.6670.0030.671
compareProtoCor1.4600.0121.473
compute.pairw.cor.meta1.7970.0271.826
compute.proto.cor.meta1.6290.3251.953
cordiff.dep0.1260.0000.126
endoPredict0.1250.0040.129
fuzzy.ttest0.1280.0000.129
gene700.2790.0040.283
gene760.1410.0000.140
geneid.map0.1370.0000.136
genius0.2430.0040.248
ggi0.1170.0120.130
ihc40.1240.0000.124
intrinsic.cluster0.3900.1800.556
intrinsic.cluster.predict0.1720.0360.208
map.datasets1.3660.1161.482
molecular.subtyping2.3710.0562.428
npi0.0940.0080.102
oncotypedx0.1130.0040.117
ovcAngiogenic0.1360.0040.141
ovcCrijns0.1210.0000.120
ovcTCGA0.2270.0040.232
ovcYoshihara0.1160.0040.120
pik3cags0.1050.0070.113
power.cor0.0000.0000.001
ps.cluster0.3740.0070.358
read.m.file0.0230.0010.023
rename.duplicate0.0020.0000.001
rescale0.2450.0070.251
rorS0.1680.0080.176
setcolclass.df0.0010.0000.001
sig.score0.1210.0000.121
spearmanCI0.0010.0000.000
st.gallen0.1540.0040.158
stab.fs0.0650.0000.065
stab.fs.ranking0.4640.0240.489
strescR0.0000.0000.001
subtype.cluster0.6900.0240.715
subtype.cluster.predict0.2880.0030.292
tamr130.1490.0010.148
tbrm000
weighted.meanvar000
write.m.file0.0040.0000.004