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CHECK report for aCGH on malbec1

This page was generated on 2020-04-15 12:04:13 -0400 (Wed, 15 Apr 2020).

Package 13/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
aCGH 1.64.0
Peter Dimitrov
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/aCGH
Branch: RELEASE_3_10
Last Commit: 42470b5
Last Changed Date: 2019-10-29 13:07:30 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: aCGH
Version: 1.64.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:aCGH.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings aCGH_1.64.0.tar.gz
StartedAt: 2020-04-15 00:12:16 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:13:36 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 80.1 seconds
RetCode: 0
Status:  OK 
CheckDir: aCGH.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:aCGH.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings aCGH_1.64.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/aCGH.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.64.0’
* 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-3.10-bioc/meat/aCGH.Rcheck/00check.log’
for details.



Installation output

aCGH.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL aCGH
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘aCGH’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/lib -L/usr/local/lib -o aCGH.so hmm.o -lm -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-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
aCGH2.0840.0242.226
aCGH.process0.0560.0040.062
aCGH.read.Sprocs0.2320.0080.255
clusterGenome1.5680.0521.626
colorectal0.3880.0000.388
fga.func0.3280.0200.345
find.hmm.states0.5200.0160.537
gainLoss0.9040.0200.924
heatmap0.5560.0160.574
impute.HMM0.6680.0000.672
impute.lowess0.0560.0040.061
mergeLevels0.1040.0040.106
plotFreqStat4.3240.0204.356
plotGenome1.6600.0401.706
plotHmmStates0.3080.0080.318
plotSummaryProfile1.0320.0161.049
summarize.clones0.3400.0000.346
threshold.func0.2040.0040.210