exomeCopy 1.18.0
Michael Love
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/exomeCopy | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | 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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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings exomeCopy_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/exomeCopy.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘exomeCopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exomeCopy’ version ‘1.18.0’
* 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 ‘exomeCopy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
emFn : <anonymous>: no visible global function definition for ‘dnbinom’
exomeCopy: no visible global function definition for ‘lm’
exomeCopy: no visible global function definition for ‘optim’
exomeCopy: no visible global function definition for ‘Rle’
getGCcontent: no visible global function definition for
‘letterFrequency’
plot.ExomeCopy: no visible global function definition for ‘segments’
plot.ExomeCopy: no visible global function definition for ‘legend’
plotCompiledCNV: no visible global function definition for ‘axis’
plotCompiledCNV: no visible global function definition for ‘segments’
plot,ExomeCopy-missing: no visible global function definition for
‘segments’
plot,ExomeCopy-missing: no visible global function definition for
‘legend’
Undefined global functions or variables:
Rle axis dnbinom legend letterFrequency lm optim segments
Consider adding
importFrom("graphics", "axis", "legend", "segments")
importFrom("stats", "dnbinom", "lm", "optim")
to your NAMESPACE file.
* 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 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
Examples with CPU or elapsed time > 5s
user system elapsed
plot.exomeCopyObject 5.809 0.000 5.834
compileCopyCountSegments 5.778 0.024 5.807
exomeCopy 5.648 0.004 5.706
plotCompiledCNV 5.578 0.000 5.623
copyCountSegments 5.491 0.019 5.625
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.3-bioc/meat/exomeCopy.Rcheck/00check.log’
for details.
* installing *source* package ‘exomeCopy’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c exomeCopy.c -o exomeCopy.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o exomeCopy.so exomeCopy.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/exomeCopy.Rcheck/exomeCopy/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (exomeCopy)