aCGH 1.48.0
Peter Dimitrov
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/aCGH | | Last Changed Rev: 109589 / Revision: 110496 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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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_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/aCGH.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aCGH/DESCRIPTION’ ... OK
* this is package ‘aCGH’ version ‘1.48.0’
* 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 ... [5s/86s] 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’
* 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 ... [20s/165s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotFreqStat 4.824 0.059 10.287
aCGH 2.590 0.154 21.074
plotGenome 1.670 0.138 53.906
clusterGenome 1.506 0.153 45.626
plotSummaryProfile 1.222 0.054 6.822
mergeLevels 0.097 0.003 6.045
* 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-3.2-bioc/meat/aCGH.Rcheck/00check.log’
for details.
* installing *source* package ‘aCGH’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -g3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c hmm.cpp -o hmm.o
llvm-g++-4.2 -arch x86_64 -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 -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-3.2-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)