BioC 2.11: CHECK report for maigesPack on lamb1

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/maigesPack.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maigesPack/DESCRIPTION’ ... OK
* this is package ‘maigesPack’ version ‘1.22.0’
* 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 whether package ‘maigesPack’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated 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 ... 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 examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
boxplot-methods 159.153  3.932 164.447
normScaleLimma  152.809  3.132 158.585
normScaleMarray  57.728  1.528  59.461
plot-methods      9.061  0.060   9.339
image-methods     5.388  0.008   5.411
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘maigesPack’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Minfo.c -o Minfo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c bootstrapT.c -o bootstrapT.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c robustCorr.c -o robustCorr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c stats.c -o stats.o
stats.c: In function ‘stats_median_from_sorted_data’:
stats.c:80:22: warning: operation on ‘i’ may be undefined [-Wsequence-point]
gcc -std=gnu99 -shared -L/usr/local/lib64 -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/maigesPack.Rcheck/maigesPack/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘show’ when loading ‘limma’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘maigesPack_tutorial.Rnw’ 
** testing if installed package can be loaded
Warning: replacing previous import ‘show’ when loading ‘limma’

* DONE (maigesPack)

name	user	system	elapsed
MI	0.004	0.000	0.004
activeMod	3.000	0.044	3.132
activeModScoreHTML	1.472	0.008	1.538
activeNet	4.392	0.000	4.397
activeNetScoreHTML	4.404	0.000	4.410
addGeneGrps	0	0	0
addPaths	0	0	0
bootstrapCor	0.040	0.000	0.042
bootstrapMI	0.237	0.000	0.236
bootstrapT	0.004	0.000	0.004
boxplot-methods	159.153	3.932	164.447
bracketMethods	0.248	0.012	0.271
calcA	0.164	0.096	0.258
calcW	0.176	0.080	0.257
classifyKNN	0.281	0.004	0.300
classifyKNNsc	0.384	0.008	0.395
classifyLDA	1.288	0.004	1.296
classifyLDAsc	2.260	0.000	2.263
classifySVM	0.752	0.008	0.780
classifySVMsc	1.292	0.012	1.305
coerce-methods	0.144	0.024	0.189
compCorr	0	0	0
createMaigesRaw	0.384	0.004	0.388
deGenes2by2BootT	0.556	0.004	0.558
deGenes2by2Ttest	0.452	0.008	0.458
deGenes2by2Wilcox	0.252	0.004	0.274
deGenesANOVA	0.252	0.024	0.281
designANOVA	0.128	0.004	0.159
dim-methods	0.064	0.008	0.079
getLabels	0.072	0.012	0.101
hierM	1.648	0.020	1.673
hierMde	0.496	0.012	0.553
image-methods	5.388	0.008	5.411
kmeansM	2.181	0.016	2.228
kmeansMde	0.504	0.008	0.594
loadData	0	0	0
normLoc	2.956	0.008	3.187
normOLIN	0.064	0.000	0.076
normRepLoess	0.064	0.004	0.072
normScaleLimma	152.809	3.132	158.585
normScaleMarray	57.728	1.528	59.461
plot-methods	9.061	0.060	9.339
plotGenePair	0.108	0.008	0.115
print-methods	0.152	0.004	0.156
relNet2TGF	0.144	0.004	0.152
relNetworkB	2.116	0.024	2.162
relNetworkM	0.096	0.004	0.115
robustCorr	0.004	0.000	0.001
selSpots	0.328	0.028	0.363
show-methods	0.148	0.004	0.152
somM	1.988	0.036	2.238
somMde	0.500	0.008	0.537
summarizeReplicates	2.880	0.016	2.901
summary-methods	0.160	0.012	0.178
tableClass	1.092	0.004	1.098
tablesDE	4.704	0.052	4.958

Summary

Command output