BioC 2.12: CHECK report for genefilter on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/genefilter.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefilter/DESCRIPTION’ ... OK
* this is package ‘genefilter’ version ‘1.42.0’
* 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 ‘genefilter’ can be installed ... [20s/21s] WARNING
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/home/biocbuild/bbs-2.12-bioc/meat/genefilter.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package 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 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 ... NOTE
eSetFilter : buildGUI: no visible binding for '<<-' assignment to ‘END’
eSetFilter : buildGUI : finish: no visible binding for '<<-' assignment
  to ‘END’
eSetFilter : buildGUI: no visible binding for global variable ‘END’
* 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 ... [36s/37s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
rowFtests       13.797  0.100  13.938
half.range.mode  6.433  0.008   6.468
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘RColorBrewer’
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/genefilter.Rcheck/00check.log’
for details.

* installing *source* package ‘genefilter’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c half_range_mode.cpp -o half_range_mode.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c nd.c -o nd.o
nd.c: In function ‘gf_dist_binary’:
nd.c:242:16: warning: unused variable ‘w2’ [-Wunused-variable]
nd.c:242:12: warning: unused variable ‘w1’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c pAUC.c -o pAUC.o
pAUC.c: In function ‘pAUC_c’:
pAUC.c:73:9: warning: operation on ‘ta’ may be undefined [-Wsequence-point]
pAUC.c:76:6: warning: operation on ‘ta’ may be undefined [-Wsequence-point]
pAUC.c:79:9: warning: operation on ‘ta’ may be undefined [-Wsequence-point]
pAUC.c: In function ‘pAUC’:
pAUC.c:141:5: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
pAUC.c:123:9: warning: unused variable ‘i’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rowPAUCs.c -o rowPAUCs.o
rowPAUCs.c: In function ‘ROCpAUC_c’:
rowPAUCs.c:97:9: warning: operation on ‘ta’ may be undefined [-Wsequence-point]
rowPAUCs.c:100:6: warning: operation on ‘ta’ may be undefined [-Wsequence-point]
rowPAUCs.c:103:9: warning: operation on ‘ta’ may be undefined [-Wsequence-point]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rowttests.c -o rowttests.o
gfortran   -fpic  -g -O2  -Wall -c ttest.f -o ttest.o
ttest.f:47.12:

         dm=dm1-dm2                                                     
            1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
ttest.f:50.12:

         dm=dm1/dm2                                                     
            1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
ttest.f:59.13:

         tst=(dm1-dm2)/sqrt((1.d0/ng1+1.d0/ng2)*(dss1+dss2)/(ng1+ng2-2))
             1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
ttest.f:62.10:

      tst=(dm1-dm2)/sqrt(dss1/((ng1-1)*ng1)+dss2/((ng2-1)*ng2))         
          1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
g++ -shared -L/usr/local/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/genefilter.Rcheck/genefilter/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘genefilter’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genefilter)

name	user	system	elapsed
Anova	0.040	0.004	0.047
allNA	0.016	0.000	0.014
coxfilter	0.124	0.004	0.195
cv	0.016	0.000	0.014
dist2	0.040	0.000	0.071
eSetFilter	0.012	0.000	0.014
filter_volcano	0.008	0.000	0.008
filtered_p	0.016	0.000	0.012
filterfun	0.024	0.000	0.025
findLargest	1.212	0.048	1.260
gapFilter	0.048	0.000	0.050
genefilter	0.060	0.000	0.057
genefinder	0.724	0.024	0.748
genescale	0.032	0.000	0.033
half.range.mode	6.433	0.008	6.468
kOverA	0.028	0.000	0.029
kappa_p	0.020	0.000	0.019
maxA	0.036	0.004	0.037
nsFilter	0.824	0.040	0.892
pOverA	0.036	0.000	0.035
rejection_plot	0.012	0.004	0.018
rowFtests	13.797	0.100	13.938
rowROC-class	0.240	0.008	0.248
rowSds	0.028	0.000	0.027
rowpAUCs	2.952	0.012	2.965
shorth	0.020	0.000	0.021
tdata	0.008	0.000	0.006
ttest	0.032	0.000	0.032

BioC 2.12: CHECK report for genefilter on george2

Summary

Command output