twilight 1.52.0
Stefanie Scheid
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/twilight | | Branch: RELEASE_3_5 | | Last Commit: ef78b78 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings twilight_1.52.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/twilight.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘twilight/DESCRIPTION’ ... OK
* this is package ‘twilight’ version ‘1.52.0’
* 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 ‘twilight’ can be installed ... OK
* 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’ ‘stats’
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
Package in Depends field not imported from: ‘splines’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
twilight: no visible global function definition for ‘makeCluster’
twilight: no visible global function definition for ‘clusterEvalQ’
twilight: no visible binding for '<<-' assignment to
‘.twilight.lambda.xxx’
twilight: no visible binding for '<<-' assignment to
‘.twilight.pval.xxx’
twilight: no visible binding for '<<-' assignment to
‘.twilight.score.xxx’
twilight: no visible global function definition for ‘clusterExport’
twilight: no visible global function definition for ‘parCapply’
twilight: no visible binding for global variable ‘.twilight.lambda.xxx’
twilight: no visible binding for global variable ‘.twilight.pval.xxx’
twilight: no visible binding for global variable ‘.twilight.score.xxx’
twilight: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
.twilight.lambda.xxx .twilight.pval.xxx .twilight.score.xxx
clusterEvalQ clusterExport makeCluster parCapply stopCluster
* 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 GNU extensions in Makefiles ... OK
* checking compiled code ... NOTE
File ‘twilight/libs/twilight.so’:
Found ‘_rand’, possibly from ‘rand’ (C)
Object: ‘sep.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
‘Rplots.pdf’
Please remove them from your package.
* checking examples ... 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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/twilight.Rcheck/00check.log’
for details.
* installing *source* package ‘twilight’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c confidence.line.c -o confidence.line.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c correlation.c -o correlation.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c kstest.c -o kstest.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c sep.c -o sep.o
sep.c:70:16: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
ix[randnum]=fabs(1-ix[randnum]);
^
sep.c:70:16: note: use function 'abs' instead
ix[randnum]=fabs(1-ix[randnum]);
^˜˜˜
abs
sep.c:97:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
ix[randnum]=fabs(1-ix[randnum]);
^
sep.c:97:20: note: use function 'abs' instead
ix[randnum]=fabs(1-ix[randnum]);
^˜˜˜
abs
sep.c:116:19: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
ix[randnum]=fabs(1-ix[randnum]);
^
sep.c:116:19: note: use function 'abs' instead
ix[randnum]=fabs(1-ix[randnum]);
^˜˜˜
abs
sep.c:143:16: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
ix[randnum]=fabs(1-ix[randnum]);
^
sep.c:143:16: note: use function 'abs' instead
ix[randnum]=fabs(1-ix[randnum]);
^˜˜˜
abs
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c twosample.perm.c -o twosample.perm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c twosample.single.c -o twosample.single.o
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 twilight.so confidence.line.o correlation.o kstest.o sep.o twosample.perm.o twosample.single.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/twilight.Rcheck/twilight/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 (twilight)