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CHECK report for aCGH on veracruz1

This page was generated on 2018-04-12 13:31:24 -0400 (Thu, 12 Apr 2018).

Package 11/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
aCGH 1.56.0
Peter Dimitrov
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/aCGH
Branch: RELEASE_3_6
Last Commit: f3531ec
Last Changed Date: 2017-10-30 12:39:02 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: aCGH
Version: 1.56.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings aCGH_1.56.0.tar.gz
StartedAt: 2018-04-12 00:08:40 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:09:56 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 75.8 seconds
RetCode: 0
Status:  OK 
CheckDir: aCGH.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings aCGH_1.56.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/aCGH.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aCGH/DESCRIPTION’ ... OK
* this is package ‘aCGH’ version ‘1.56.0’
* 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 ... OK
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/aCGH.Rcheck/00check.log’
for details.



Installation output

aCGH.Rcheck/00install.out

* installing *source* package ‘aCGH’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -g3  -I/usr/local/include   -fPIC  -Wall -g -O2  -c hmm.cpp -o hmm.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/aCGH.Rcheck/aCGH/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (aCGH)

Tests output


Example timings

aCGH.Rcheck/aCGH-Ex.timings

nameusersystemelapsed
aCGH2.1480.1132.299
aCGH.process0.0790.0010.084
aCGH.read.Sprocs0.3120.0040.324
clusterGenome1.1800.0671.276
colorectal0.4820.0240.517
fga.func0.4100.0170.432
find.hmm.states0.3990.0140.414
gainLoss0.9170.0250.944
heatmap0.3380.0220.362
impute.HMM0.3970.0070.406
impute.lowess0.1070.0020.108
mergeLevels0.0800.0020.082
plotFreqStat3.4250.0373.482
plotGenome1.1390.0581.237
plotHmmStates0.2250.0270.253
plotSummaryProfile0.8260.0460.890
summarize.clones0.2520.0270.279
threshold.func0.1580.0190.177