Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-23 12:05:15 -0400 (Mon, 23 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for genefu on nebbiolo1


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? 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 744/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefu 2.28.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2022-05-22 13:55:15 -0400 (Sun, 22 May 2022)
git_url: https://git.bioconductor.org/packages/genefu
git_branch: RELEASE_3_15
git_last_commit: f2f0027
git_last_commit_date: 2022-04-26 11:07:23 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / 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: 2.28.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings genefu_2.28.0.tar.gz
StartedAt: 2022-05-22 19:40:00 -0400 (Sun, 22 May 2022)
EndedAt: 2022-05-22 19:42:27 -0400 (Sun, 22 May 2022)
EllapsedTime: 147.7 seconds
RetCode: 0
Status:   OK  
CheckDir: genefu.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings genefu_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/genefu.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘2.28.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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  5.1Mb
  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 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-3.15-bioc/meat/genefu.Rcheck/00check.log’
for details.



Installation output

genefu.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL genefu
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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
bimod0.1930.0080.201
boxplotplus20.0070.0000.007
claudinLow1.0270.0801.107
compareProtoCor1.2320.0121.244
compute.pairw.cor.meta1.3770.0081.384
compute.proto.cor.meta1.0850.0481.133
cordiff.dep0.1020.0040.105
endoPredict0.1010.0080.109
fuzzy.ttest0.0850.0000.086
gene700.2530.0160.270
gene760.1150.0040.118
geneid.map0.1350.0000.135
genius0.2010.0360.236
ggi0.1070.0120.119
ihc40.1140.0160.130
intrinsic.cluster0.3540.0120.352
intrinsic.cluster.predict0.1560.0080.164
map.datasets1.1970.0521.249
molecular.subtyping1.8160.0401.862
npi0.1080.0160.125
oncotypedx0.1180.0120.130
ovcAngiogenic0.1260.0000.126
ovcCrijns0.1240.0030.127
ovcTCGA0.2650.0090.273
ovcYoshihara0.1140.0150.130
pik3cags0.1280.0000.128
power.cor0.0000.0000.001
ps.cluster0.4090.0110.399
read.m.file0.0180.0030.022
rename.duplicate0.0000.0020.002
rescale0.2350.0010.236
rorS0.1620.0080.169
setcolclass.df0.0010.0000.002
sig.score0.1260.0040.129
spearmanCI0.0000.0000.001
st.gallen0.1120.0040.115
stab.fs0.0850.0000.085
stab.fs.ranking0.5550.0720.627
strescR0.0010.0000.001
subtype.cluster0.6520.0240.676
subtype.cluster.predict0.2620.0040.267
tamr130.1310.0040.135
tbrm0.0000.0000.001
weighted.meanvar0.0000.0000.001
write.m.file0.0030.0000.004