Package: maanova

Version: 1.54.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:maanova.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings maanova_1.54.0.tar.gz

StartedAt: 2019-10-16 04:11:13 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:12:20 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 67.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: maanova.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:maanova.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings maanova_1.54.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/maanova.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 ‘maanova/DESCRIPTION’ ... OK
* this is package ‘maanova’ version ‘1.54.0’
* 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 ‘maanova’ can be installed ... WARNING
Found the following significant warnings:
  shift.c:48:17: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/maanova.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘qvalue’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.consensus.hc plot.consensus.kmean print.madata
  print.summary.madata print.summary.mamodel subset.madata
  summary.madata summary.mamodel transform.madata transform.rawdata
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
fdr: no visible global function definition for ‘qvalue’
matest: no visible global function definition for ‘makeMPIcluster’
matest: no visible global function definition for ‘clusterApply’
matest: no visible global function definition for ‘clusterEvalQ’
matest: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
  clusterApply clusterEvalQ makeMPIcluster qvalue 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/maanova.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 maanova
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘maanova’ ...
** 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 makeratio.c -o makeratio.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 masvd.c -o masvd.o
masvd.c:114:2: warning: '/*' within block comment [-Wcomment]
        /* work on a copy of x */
        ^
masvd.c:154:1: warning: '/*' within block comment [-Wcomment]
/*#ifndef IEEE_754
^
masvd.c:161:5: warning: '/*' within block comment [-Wcomment]
    /* work on a copy of x */
    ^
masvd.c:165:2: warning: '/*' within block comment [-Wcomment]
        /* ask for optimal size of work array */
        ^
masvd.c:189:2: warning: '/*' within block comment [-Wcomment]
        /* ask for optimal size of work array */
        ^
5 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 shift.c -o shift.o
shift.c:48:17: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
      sad[i] += abs(x[j]-med);
                ^
shift.c:48:17: note: use function 'fabs' instead
      sad[i] += abs(x[j]-med);
                ^~~
                fabs
shift.c:27:13: warning: unused variable 'k' [-Wunused-variable]
  int i, j, k;
            ^
2 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 util.c -o util.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 maanova.so makeratio.o masvd.o shift.o util.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-maanova/00new/maanova/libs
** R
** data
** demo
** 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 (maanova)

name	user	system	elapsed
PairContrast	0.100	0.007	0.106
Rmaanova.version	0.007	0.001	0.010
abf1	0.009	0.005	0.014
adjPval	0.009	0.005	0.015
arrayview	0.000	0.000	0.001
consensus	0.007	0.004	0.012
dyeswapfilter	0.001	0.001	0.001
fill.missing	0.187	0.056	0.243
fitmaanova	0.006	0.004	0.010
fom	0.006	0.004	0.010
geneprofile	0.007	0.003	0.010
gridcheck	0.000	0.000	0.001
kidney	0.050	0.011	0.062
maanova-internal	0.003	0.002	0.005
macluster	0.006	0.004	0.011
matest	0.006	0.005	0.010
read.madata	0	0	0
resiplot	0.007	0.005	0.011
riplot	0.000	0.000	0.001
subset.madata	0.048	0.010	0.059
summarytable	0.007	0.005	0.011
transform.madata	0.047	0.009	0.056
varplot	0.006	0.004	0.010
volcano	0.000	0.000	0.001
write.madata	0.007	0.006	0.013