genefilter 1.46.1
Bioconductor Package Maintainer
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/genefilter | | Last Changed Rev: 90176 / Revision: 95116 | | Last Changed Date: 2014-05-09 15:54:26 -0700 (Fri, 09 May 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | 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 | [ 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 --no-multiarch genefilter_1.46.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/genefilter.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefilter/DESCRIPTION’ ... OK
* this is package ‘genefilter’ version ‘1.46.1’
* 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 ... [11s/11s] WARNING
Found the following significant warnings:
pAUC.c:73:15: warning: multiple unsequenced modifications to 'ta' [-Wunsequenced]
pAUC.c:76:12: warning: multiple unsequenced modifications to 'ta' [-Wunsequenced]
pAUC.c:79:15: warning: multiple unsequenced modifications to 'ta' [-Wunsequenced]
rowPAUCs.c:97:15: warning: multiple unsequenced modifications to 'ta' [-Wunsequenced]
rowPAUCs.c:100:12: warning: multiple unsequenced modifications to 'ta' [-Wunsequenced]
rowPAUCs.c:103:15: warning: multiple unsequenced modifications to 'ta' [-Wunsequenced]
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Users/biocbuild/bbs-2.14-bioc/meat/genefilter.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’ ‘methods’
A package should be listed in only one of these fields.
* 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
':::' call which should be '::': ‘tkWidgets:::formatArg’
See the note in ?`:::` about the use of this operator.
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 ... NOTE
Call with DUP = FALSE:
.C("gf_distance", X = as.double(X), nr = as.integer(N), nc = ncol(X),
g = as.integer(Genes), d = as.double(Dists), iRow = as.integer(iRows),
nInterest = as.integer(ninterest), nResults = as.integer(numResults),
method = as.integer(method), weights = as.double(weights),
DUP = FALSE, NAOK = TRUE, PACKAGE = "genefilter")
DUP = FALSE is deprecated and may be disabled in future versions of R.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
rowFtests 7.082 0.074 7.202
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/genefilter.Rcheck/00check.log’
for details.
* installing *source* package ‘genefilter’ ...
** 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 half_range_mode.cpp -o half_range_mode.o
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 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 -fPIC -Wall -mtune=core2 -g -O2 -c nd.c -o nd.o
nd.c:242:12: warning: unused variable 'w1' [-Wunused-variable]
double w1, w2; /* Weighted values */
^
nd.c:242:16: warning: unused variable 'w2' [-Wunused-variable]
double w1, w2; /* Weighted values */
^
2 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 pAUC.c -o pAUC.o
pAUC.c:73:15: warning: multiple unsequenced modifications to 'ta' [-Wunsequenced]
ta = ta += ((x[i]-(*p))*(y[i]-y[i-1])/2) + ((x[i]-(*p))*y[i-1]);
˜ ^
pAUC.c:76:12: warning: multiple unsequenced modifications to 'ta' [-Wunsequenced]
ta = ta += ((x[i]-x[i-1])*(y[i]-y[i-1])/2) + ((x[i]-x[i-1])*y[i-1]);
˜ ^
pAUC.c:79:15: warning: multiple unsequenced modifications to 'ta' [-Wunsequenced]
ta = ta += ((1-x[i-1])*(1-y[i-1])/2) + ((1-x[i-1])*y[i-1]);
˜ ^
pAUC.c:123:9: warning: unused variable 'i' [-Wunused-variable]
int i;
^
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 rowPAUCs.c -o rowPAUCs.o
rowPAUCs.c:97:15: warning: multiple unsequenced modifications to 'ta' [-Wunsequenced]
ta = ta += ((x[i]-(*p))*(y[i]-y[i-1])/2) + ((x[i]-(*p))*y[i-1]);
˜ ^
rowPAUCs.c:100:12: warning: multiple unsequenced modifications to 'ta' [-Wunsequenced]
ta = ta += ((x[i]-x[i-1])*(y[i]-y[i-1])/2) + ((x[i]-x[i-1])*y[i-1]);
˜ ^
rowPAUCs.c:103:15: warning: multiple unsequenced modifications to 'ta' [-Wunsequenced]
ta = ta += ((1-x[i-1])*(1-y[i-1])/2) + ((1-x[i-1])*y[i-1]);
˜ ^
3 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 rowttests.c -o rowttests.o
gfortran-4.8 -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)
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-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)