Multiple platform build/check report for BioC 3.9 - CHECK report for twilight on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:twilight.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings twilight_1.60.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/twilight.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.60.0’
* 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 ... WARNING
Found the following significant warnings:
  sep.c:70:16: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  sep.c:97:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  sep.c:116:19: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  sep.c:143:16: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/twilight.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’ ‘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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.twilight print.twilight
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/twilight/libs/twilight.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘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: 1 WARNING, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/twilight.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL twilight
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘twilight’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c correlation.c -o correlation.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c kstest.c -o kstest.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-twilight/00new/twilight/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (twilight)

name	user	system	elapsed
plot.twilight	0.173	0.033	0.355
print.twilight	0.058	0.011	0.118
twilight	0.148	0.026	0.291
twilight.combi	0.019	0.002	0.035
twilight.filtering	0.001	0.000	0.002
twilight.pval	0.102	0.017	0.193
twilight.teststat	0.006	0.002	0.009

CHECK report for twilight on celaya2

Summary

Command output

Installation output

Tests output

Example timings