gaga 2.14.0
David Rossell
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/gaga | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| 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 | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | 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 gaga_2.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/gaga.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaga/DESCRIPTION’ ... OK
* this is package ‘gaga’ version ‘2.14.0’
* 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 ‘gaga’ can be installed ... [8s/8s] 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
‘EBarrays’ ‘mgcv’
Please remove these calls from your code.
Packages in Depends field not imported from:
‘Biobase’ ‘EBarrays’ ‘coda’ ‘mgcv’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘makeEBarraysSingleHyp’ ‘sigmaPriorEst’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
adjustfitNN: no visible global function definition for ‘gam’
checkfit.gagafit: no visible global function definition for ‘pData’
checkfit.gagafit: no visible global function definition for ‘exprs’
checkfit.gagafit: no visible global function definition for ‘fData’
classpred.gagafit: no visible global function definition for ‘pData’
classpred.gagafit: no visible global function definition for ‘exprs’
findgenes.gagafit: no visible global function definition for ‘pData’
findgenes.gagafit: no visible global function definition for ‘exprs’
fitGG: no visible global function definition for ‘pData’
fitGG: no visible global function definition for ‘exprs’
fitGG: no visible global function definition for ‘as.mcmc’
fitNN: no visible global function definition for ‘pData’
fitNN: no visible global function definition for ‘exprs’
fitNN: no visible global function definition for ‘eb.createFamilyLNNMV’
fitNN: no visible global function definition for ‘emfit’
fitNN: no visible global function definition for ‘postprob’
fitNNSingleHyp: no visible global function definition for ‘pData’
fitNNSingleHyp: no visible global function definition for ‘exprs’
forwsimDiffExpr.gagafit: no visible global function definition for
‘pData’
forwsimDiffExpr.gagafit: no visible global function definition for
‘exprs’
forwsimDiffExpr.nnfit: no visible global function definition for
‘pData’
forwsimDiffExpr.nnfit: no visible global function definition for
‘exprs’
forwsimDiffExpr.nnfit: no visible global function definition for
‘fData’
makeEBarraysHyp: no visible global function definition for ‘ebPatterns’
parest.gagafit: no visible global function definition for ‘pData’
parest.gagafit: no visible global function definition for ‘exprs’
parest.gagafit: no visible global function definition for ‘mcmc’
posmeansGG.gagafit: no visible global function definition for ‘pData’
posmeansGG.gagafit: no visible global function definition for ‘exprs’
powclasspred.gagafit: no visible global function definition for ‘pData’
powclasspred.gagafit: no visible global function definition for ‘exprs’
powfindgenes.gagafit: no visible global function definition for ‘pData’
powfindgenes.gagafit: no visible global function definition for ‘exprs’
powfindgenes.nnfit: no visible global function definition for ‘pData’
powfindgenes.nnfit: no visible global function definition for ‘exprs’
powfindgenes.nnfit : f: no visible global function definition for
‘exprs’
powsimprior.nnfit : f: no visible global function definition for
‘exprs’
ppGG: no visible global function definition for ‘pData’
ppGG: no visible global function definition for ‘exprs’
sigmaPriorEst: no visible global function definition for ‘exprs’
simGG: no visible global function definition for ‘sampleNames<-’
simGG: no visible global function definition for ‘varLabels<-’
simLNN: no visible global function definition for ‘exprs<-’
simLNN: no visible global function definition for ‘exprs’
simnewsamples.gagafit: no visible global function definition for
‘pData’
simnewsamples.gagafit: no visible global function definition for
‘exprs’
simnewsamples.gagafit: no visible global function definition for
‘sampleNames<-’
simnewsamples.gagafit: no visible global function definition for
‘varLabels<-’
simnewsamples.nnfit: no visible global function definition for ‘pData’
simnewsamples.nnfit: no visible global function definition for ‘exprs’
simnewsamples.nnfit: no visible global function definition for
‘sampleNames<-’
simnewsamples.nnfit: no visible global function definition for
‘varLabels<-’
updateNNfit: no visible global function definition for ‘postprob’
* 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 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 ... [5s/5s] 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/gaga.Rcheck/00check.log’
for details.
* installing *source* package ‘gaga’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c cseqdesma.c -o cseqdesma.o
cseqdesma.c:4524:14: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*usesumx==0)) { //if suff stat not pre-computed
˜˜˜˜˜˜˜˜^˜˜
cseqdesma.c:4524:14: note: remove extraneous parentheses around the comparison to silence this warning
if ((*usesumx==0)) { //if suff stat not pre-computed
˜ ^ ˜
cseqdesma.c:4524:14: note: use '=' to turn this equality comparison into an assignment
if ((*usesumx==0)) { //if suff stat not pre-computed
^˜
=
cseqdesma.c:5836:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*usel==0)) {
˜˜˜˜˜^˜˜
cseqdesma.c:5836:13: note: remove extraneous parentheses around the comparison to silence this warning
if ((*usel==0)) {
˜ ^ ˜
cseqdesma.c:5836:13: note: use '=' to turn this equality comparison into an assignment
if ((*usel==0)) {
^˜
=
cseqdesma.c:6070:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*usel==0)) {
˜˜˜˜˜^˜˜
cseqdesma.c:6070:13: note: remove extraneous parentheses around the comparison to silence this warning
if ((*usel==0)) {
˜ ^ ˜
cseqdesma.c:6070:13: note: use '=' to turn this equality comparison into an assignment
if ((*usel==0)) {
^˜
=
cseqdesma.c:6340:13: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((*usel==0)) { //If l values have to be generated
˜˜˜˜˜^˜˜
cseqdesma.c:6340:13: note: remove extraneous parentheses around the comparison to silence this warning
if ((*usel==0)) { //If l values have to be generated
˜ ^ ˜
cseqdesma.c:6340:13: note: use '=' to turn this equality comparison into an assignment
if ((*usel==0)) { //If l values have to be generated
^˜
=
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c cstat.c -o cstat.o
cstat.c:18:19: warning: unused variable 'interface_c_sccs_id' [-Wunused-const-variable]
static const char interface_c_sccs_id[] = "%W%";
^
cstat.c:19:19: warning: unused variable 'mess_c_sccs_id' [-Wunused-const-variable]
static const char mess_c_sccs_id[] = "%W%";
^
cstat.c:20:19: warning: unused variable 'nrutil_c_sccs_id' [-Wunused-const-variable]
static const char nrutil_c_sccs_id[] = "%W%";
^
cstat.c:21:19: warning: unused variable 'vector_c_sccs_id' [-Wunused-const-variable]
static const char vector_c_sccs_id[] = "%W%";
^
cstat.c:22:19: warning: unused variable 'css_c_sccs_id' [-Wunused-const-variable]
static const char css_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$";
^
5 warnings generated.
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 gaga.so cseqdesma.o cstat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/gaga.Rcheck/gaga/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gaga)