Package: aCGH

Version: 1.58.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:aCGH.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings aCGH_1.58.0.tar.gz

StartedAt: 2018-10-16 19:46:55 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 19:48:28 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 92.6 seconds

RetCode: 0

Status:  OK

CheckDir: aCGH.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:aCGH.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings aCGH_1.58.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/aCGH.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.58.0’
* 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/aCGH.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL aCGH
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* 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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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
* DONE (aCGH)

name	user	system	elapsed
aCGH	2.178	0.164	2.365
aCGH.process	0.068	0.002	0.070
aCGH.read.Sprocs	0.245	0.006	0.262
clusterGenome	1.205	0.094	1.318
colorectal	0.338	0.039	0.393
fga.func	0.413	0.037	0.453
find.hmm.states	0.598	0.029	0.633
gainLoss	0.887	0.039	0.932
heatmap	0.344	0.032	0.376
impute.HMM	0.493	0.007	0.505
impute.lowess	0.104	0.001	0.108
mergeLevels	0.083	0.002	0.086
plotFreqStat	4.144	0.060	4.235
plotGenome	1.267	0.080	1.370
plotHmmStates	0.301	0.036	0.342
plotSummaryProfile	1.048	0.061	1.128
summarize.clones	0.455	0.041	0.503
threshold.func	0.195	0.024	0.221