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This page was generated on 2021-12-01 17:17:25 -0500 (Wed, 01 Dec 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 2.26.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/genefu
git_branch: RELEASE_3_14
git_last_commit: a884b26
git_last_commit_date: 2021-10-26 11:58:39 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: genefu
Version: 2.26.0
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_2.26.0.tar.gz
StartedAt: 2021-11-30 09:15:15 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 09:17:56 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 161.1 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_2.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/genefu.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.26.0’
* 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 ... 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
bimod0.2370.0160.253
boxplotplus20.0110.0000.010
claudinLow0.8000.0240.824
compareProtoCor1.9610.0081.969
compute.pairw.cor.meta2.1540.0162.171
compute.proto.cor.meta1.9130.0121.925
cordiff.dep0.1300.0000.131
endoPredict0.1310.0040.135
fuzzy.ttest0.1240.0000.125
gene700.2650.0240.288
gene760.1430.0000.143
geneid.map0.1320.0000.132
genius0.2430.0040.248
ggi0.1280.0000.128
ihc40.1190.0000.118
intrinsic.cluster0.5030.0080.498
intrinsic.cluster.predict0.1890.0080.197
map.datasets1.8090.0081.818
molecular.subtyping3.0740.0413.118
npi0.1100.0000.111
oncotypedx0.1200.0040.124
ovcAngiogenic0.1580.0040.163
ovcCrijns0.120.000.12
ovcTCGA0.2480.0040.251
ovcYoshihara0.1270.0000.127
pik3cags0.1240.0120.137
power.cor000
ps.cluster0.4200.0080.415
read.m.file0.0220.0000.023
rename.duplicate0.0020.0000.002
rescale0.2950.0000.294
rorS0.1850.0030.190
setcolclass.df0.0020.0000.002
sig.score0.1290.0080.137
spearmanCI0.0000.0000.001
st.gallen0.1190.0040.123
stab.fs0.0690.0000.069
stab.fs.ranking0.5340.0520.586
strescR0.0010.0000.001
subtype.cluster0.7780.0200.797
subtype.cluster.predict0.2950.0120.307
tamr130.1520.0080.160
tbrm0.0000.0000.001
weighted.meanvar000
write.m.file0.0040.0000.004