crlmm 1.20.4
Benilton S Carvalho , Robert Scharpf , Matt Ritchie
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/crlmm | | Last Changed Rev: 86688 / Revision: 88450 | | Last Changed Date: 2014-02-21 11:08:02 -0800 (Fri, 21 Feb 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/crlmm.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.20.4’
* 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 ... [20s/20s] OK
* checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
data 2.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘ellipse’ ‘VGAM’
A package should be listed in only one of these fields.
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 ... NOTE
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.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘calculateRTheta’ ‘processIDAT’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [257s/260s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
genotype 108.339 1.452 112.448
crlmm 108.223 1.100 109.548
snprma 19.953 0.428 20.446
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘crlmm_unit_tests.R’ [124s/125s]
Running ‘doRUnit.R’ [127s/129s]
[251s/254s] 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
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/crlmm.Rcheck/00check.log’
for details.
* installing *source* package ‘crlmm’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c gtypeCaller.c -o gtypeCaller.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c utils.c -o utils.o
gcc -std=gnu99 -shared -L/usr/local/lib -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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)