crlmm 1.32.0
Benilton S Carvalho
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/crlmm | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | 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 crlmm_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/crlmm.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crlmm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crlmm’ version ‘1.32.0’
* 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 ‘crlmm’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
data 2.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘preprocessCore’ is only usable in R >= 3.0.2
* 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 ... WARNING
'library' or 'require' call not declared from: ‘limma’
'library' or 'require' calls in package code:
‘RUnit’ ‘limma’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
‘SNPchip’ ‘ff’ ‘splines’
All declared Imports should be used.
Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.test: no visible global function definition for ‘defineTestSuite’
.test: no visible global function definition for ‘runTestSuite’
.test: no visible global function definition for ‘printTextProtocol’
calculateRBafCNSet : processByChromosome: no visible global function
definition for ‘position’
cnrmaAffy: no visible global function definition for ‘celfileName’
computeBR: no visible global function definition for ‘genomeBuild’
constructBafLrrSetListFrom: no visible global function definition for
‘genomeBuild’
constructOligoSetListFrom: no visible global function definition for
‘genomeBuild’
genotypeInf: no visible binding for global variable ‘anno’
plotSamples: no visible global function definition for ‘delete’
quantilenormalization: no visible global function definition for
‘delete’
snprmaAffy: no visible global function definition for ‘celfileName’
Undefined global functions or variables:
anno celfileName defineTestSuite delete genomeBuild position
printTextProtocol runTestSuite
* 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 for GNU extensions in Makefiles ... 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
crlmm 97.873 2.210 104.773
genotype 80.656 4.891 332.887
snprma 17.688 0.997 18.724
celfile-utils 3.181 0.258 11.127
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘crlmm_unit_tests.R’
Running ‘doRUnit.R’
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: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/crlmm.Rcheck/00check.log’
for details.
* installing *source* package ‘crlmm’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c gtypeCaller.c -o gtypeCaller.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c trimmed.c -o trimmed.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c utils.c -o utils.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 crlmm.so gtypeCaller.o init.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/crlmm.Rcheck/crlmm/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 (crlmm)