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CHECK report for aCGH on malbec2

This page was generated on 2019-04-09 11:23:35 -0400 (Tue, 09 Apr 2019).

Package 13/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
aCGH 1.61.0
Peter Dimitrov
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/aCGH
Branch: master
Last Commit: b218a55
Last Changed Date: 2018-10-30 11:54:26 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: aCGH
Version: 1.61.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:aCGH.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings aCGH_1.61.0.tar.gz
StartedAt: 2019-04-08 22:36:19 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 22:38:07 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 108.2 seconds
RetCode: 0
Status:  OK 
CheckDir: aCGH.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:aCGH.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings aCGH_1.61.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/aCGH.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aCGH/DESCRIPTION’ ... OK
* this is package ‘aCGH’ version ‘1.61.0’
* 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 ‘aCGH’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘cluster’ ‘multtest’ ‘survival’
A package should be listed in only one of these fields.
* 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
Missing or unexported object: ‘multtest::.mt.naNUM’
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  [.aCGH dim.aCGH plot.aCGH print.aCGH row.names.aCGH row.names<-.aCGH
  subset.hmm subset.hmm.merged summary.aCGH
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aCGH.read.Sprocs: warning in read.table(fnames[1], h = TRUE, sep =
  "\t", quote = "", comment.char = "", fill = TRUE, blank.lines.skip =
  FALSE): partial argument match of 'h' to 'header'
aCGH.read.Sprocs: warning in read.table(latest.mapping.file, sep =
  "\t", h = TRUE, quote = "", comment.char = ""): partial argument
  match of 'h' to 'header'
plotCGH.func: warning in close.screen(all = TRUE): partial argument
  match of 'all' to 'all.screens'
plotCGH.hmm.func: warning in close.screen(all = TRUE): partial argument
  match of 'all' to 'all.screens'
plotFreqStat: warning in axis(side = 1, at = kb.loc[ind][1], label =
  "", tick = FALSE): partial argument match of 'label' to 'labels'
plotGenome: warning in axis(side = 1, at = clone.genomepos[1]/1000,
  label = "", tick = FALSE): partial argument match of 'label' to
  'labels'
read.Sproc.files : <anonymous>: warning in read.table(fname, h = TRUE,
  sep = "\t", quote = "", comment.char = "", fill = TRUE,
  blank.lines.skip = FALSE, dec = "."): partial argument match of 'h'
  to 'header'
states.hmm.func: warning in matrix(res$filtered.cond.probs, nr = k):
  partial argument match of 'nr' to 'nrow'
states.hmm.func: warning in matrix(res$gamma, nr = k): partial argument
  match of 'nr' to 'nrow'
plotSummaryProfile: no visible binding for global variable
  ‘numchromgain’
plotSummaryProfile: no visible binding for global variable
  ‘numchromloss’
plotSummaryProfile: no visible binding for global variable ‘numtrans’
plotSummaryProfile: no visible binding for global variable
  ‘numtrans.binary’
plotSummaryProfile: no visible binding for global variable ‘numaber’
plotSummaryProfile: no visible binding for global variable ‘numamplif’
plotSummaryProfile: no visible binding for global variable
  ‘numamplif.binary’
plotSummaryProfile: no visible binding for global variable
  ‘numamplicon’
plotSummaryProfile: no visible binding for global variable
  ‘sizeamplicon’
Undefined global functions or variables:
  numaber numamplicon numamplif numamplif.binary numchromgain
  numchromloss numtrans numtrans.binary sizeamplicon
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/aCGH.Rcheck/00check.log’
for details.



Installation output

aCGH.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL aCGH
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘aCGH’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -g3  -I/usr/local/include  -fpic  -g -O2  -Wall -c hmm.cpp -o hmm.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o aCGH.so hmm.o -lm -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-aCGH/00new/aCGH/libs
** R
** data
** demo
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (aCGH)

Tests output


Example timings

aCGH.Rcheck/aCGH-Ex.timings

nameusersystemelapsed
aCGH1.5780.0401.634
aCGH.process0.0320.0000.032
aCGH.read.Sprocs0.3420.0000.379
clusterGenome1.5040.0641.568
colorectal0.4590.0280.488
fga.func0.2150.0040.219
find.hmm.states0.6220.0120.635
gainLoss1.1060.0041.113
heatmap0.3240.0080.332
impute.HMM0.7870.0000.787
impute.lowess0.0900.0030.093
mergeLevels0.1180.0000.118
plotFreqStat4.4880.0404.529
plotGenome1.4230.0281.451
plotHmmStates0.2520.0080.259
plotSummaryProfile0.8400.0080.850
summarize.clones0.2160.0040.220
threshold.func0.1730.0000.172