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CHECK report for multtest on malbec2

This page was generated on 2019-10-16 11:55:02 -0400 (Wed, 16 Oct 2019).

Package 1072/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multtest 2.40.0
Katherine S. Pollard
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/multtest
Branch: RELEASE_3_9
Last Commit: 5f00017
Last Changed Date: 2019-05-02 11:53:01 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: multtest
Version: 2.40.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:multtest.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings multtest_2.40.0.tar.gz
StartedAt: 2019-10-16 03:27:24 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:28:51 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 87.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: multtest.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:multtest.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings multtest_2.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/multtest.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multtest/DESCRIPTION’ ... OK
* this is package ‘multtest’ version ‘2.40.0’
* 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 ‘multtest’ can be installed ... WARNING
Found the following significant warnings:
  stat_func.c:703:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  stat_func.c:705:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  stat_func.c:710:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  stat_func.c:714:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/multtest.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 dependencies in R code ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘multtest/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

EBMTP: no visible global function definition for ‘makeCluster’
EBMTP: no visible global function definition for ‘stopCluster’
EBMTP: no visible global function definition for ‘combn’
Hsets: no visible global function definition for ‘approxfun’
Hsets: no visible global function definition for ‘rbinom’
IC.Cor.NA: no visible global function definition for ‘cov2cor’
IC.CorXW.NA: no visible global function definition for ‘cov2cor’
MTP: no visible global function definition for ‘makeCluster’
MTP: no visible global function definition for ‘stopCluster’
MTP: no visible global function definition for ‘combn’
boot.null: no visible global function definition for ‘runif’
corr.Tn: no visible global function definition for ‘cov’
corr.Tn: no visible global function definition for ‘cov2cor’
corr.null: no visible global function definition for ‘cor’
corr.null: no visible global function definition for ‘cov’
corr.null: no visible global function definition for ‘cov2cor’
corr.null: no visible global function definition for ‘lm.wfit’
corr.null: no visible global function definition for ‘combn’
corr.null: no visible global function definition for ‘rnorm’
lmX : : no visible global function definition for ‘lm.fit’
lmX : : no visible global function definition for ‘lm.wfit’
lmY : : no visible global function definition for ‘lm.fit’
lmY : : no visible global function definition for ‘lm.wfit’
marg.samp: no visible global function definition for ‘rnorm’
marg.samp: no visible global function definition for ‘rt’
marg.samp: no visible global function definition for ‘rf’
mt.legend: no visible global function definition for ‘par’
mt.legend: no visible global function definition for ‘xy.coords’
mt.legend : rect2: no visible global function definition for ‘rect’
mt.legend : segments2: no visible global function definition for
  ‘segments’
mt.legend : points2: no visible global function definition for ‘points’
mt.legend : text2: no visible global function definition for ‘text’
mt.legend: no visible global function definition for ‘strwidth’
mt.legend: no visible global function definition for ‘xinch’
mt.legend: no visible global function definition for ‘yinch’
mt.legend: no visible global function definition for ‘strheight’
mt.plot: no visible global function definition for ‘matplot’
quant.trans: no visible binding for global variable ‘quantile’
sd.maxT: no visible global function definition for ‘quantile’
sd.minP: no visible global function definition for ‘quantile’
ss.maxT: no visible global function definition for ‘quantile’
ss.minP: no visible global function definition for ‘quantile’
tQuantTrans: no visible binding for global variable ‘quantile’
EBupdate,EBMTP: no visible binding for global variable ‘y’
plot,EBMTP-ANY: no visible global function definition for ‘par’
plot,EBMTP-ANY: no visible global function definition for
  ‘dev.interactive’
plot,EBMTP-ANY: no visible global function definition for ‘matplot’
plot,EBMTP-ANY: no visible global function definition for ‘title’
plot,EBMTP-ANY: no visible global function definition for ‘mtext’
plot,MTP-ANY: no visible global function definition for ‘par’
plot,MTP-ANY: no visible global function definition for
  ‘dev.interactive’
plot,MTP-ANY: no visible global function definition for ‘matplot’
plot,MTP-ANY: no visible global function definition for ‘title’
plot,MTP-ANY: no visible global function definition for ‘mtext’
plot,MTP-ANY: no visible global function definition for ‘points’
plot,MTP-ANY: no visible global function definition for ‘text’
update,MTP: no visible binding for global variable ‘y’
Undefined global functions or variables:
  approxfun combn cor cov cov2cor dev.interactive lm.fit lm.wfit
  makeCluster matplot mtext par points quantile rbinom rect rf rnorm rt
  runif segments stopCluster strheight strwidth text title xinch
  xy.coords y yinch
Consider adding
  importFrom("grDevices", "dev.interactive", "xy.coords")
  importFrom("graphics", "matplot", "mtext", "par", "points", "rect",
             "segments", "strheight", "strwidth", "text", "title",
             "xinch", "yinch")
  importFrom("stats", "approxfun", "cor", "cov", "cov2cor", "lm.fit",
             "lm.wfit", "quantile", "rbinom", "rf", "rnorm", "rt",
             "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'EBMTP,ANY,ANY,ANY'
  generic '[' and siglist 'MTP,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/multtest/libs/multtest.so’:
  Found ‘stderr’, possibly from ‘stderr’ (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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘MTP.pdf’, ‘MTP.tex’, ‘MTPALL.pdf’, ‘golub.R’, ‘multtest.bib’,
    ‘multtest.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/multtest.Rcheck/00check.log’
for details.



Installation output

multtest.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL multtest
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘multtest’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -DUSEDOUBLE -fpic  -g -O2  -Wall -c Rpack.c -o Rpack.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -DUSEDOUBLE -fpic  -g -O2  -Wall -c VScount.c -o VScount.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -DUSEDOUBLE -fpic  -g -O2  -Wall -c block_sampling_fixed.c -o block_sampling_fixed.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -DUSEDOUBLE -fpic  -g -O2  -Wall -c bootloop.c -o bootloop.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -DUSEDOUBLE -fpic  -g -O2  -Wall -c mt.c -o mt.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -DUSEDOUBLE -fpic  -g -O2  -Wall -c pairt_sampling.c -o pairt_sampling.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -DUSEDOUBLE -fpic  -g -O2  -Wall -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -DUSEDOUBLE -fpic  -g -O2  -Wall -c random.c -o random.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -DUSEDOUBLE -fpic  -g -O2  -Wall -c sampling.c -o sampling.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -DUSEDOUBLE -fpic  -g -O2  -Wall -c sampling_fixed.c -o sampling_fixed.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -DUSEDOUBLE -fpic  -g -O2  -Wall -c stat_func.c -o stat_func.o
stat_func.c: In function ‘read_infile’:
stat_func.c:703:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fh, "%s", pdata->name);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stat_func.c:705:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fh, "%d", pdata->L+j);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
stat_func.c:710:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fh, "%s", pdata->id[i]);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stat_func.c:714:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
       fscanf(fh, "%lg",&ftemp);
       ^~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include -DUSEDOUBLE -fpic  -g -O2  -Wall -c stat_order.c -o stat_order.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o multtest.so Rpack.o VScount.o block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o stat_order.o -lm -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-multtest/00new/multtest/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 (multtest)

Tests output


Example timings

multtest.Rcheck/multtest-Ex.timings

nameusersystemelapsed
EBMTP-class000
EBMTP0.3340.0000.334
Hsets0.3390.0000.342
MTP-class0.0000.0000.001
MTP0.8910.0000.905
boot.null0.0410.0040.044
corr.null0.0290.0000.029
fwer2gfwer4.3060.0004.352
get.index0.3740.0240.398
meanX0.0110.0000.012
mt.maxT3.9580.0123.970
mt.plot0.2760.0040.280
mt.rawp2adjp0.280.000.28
mt.reject0.2990.0000.300
mt.sample.teststat0.0570.0000.058
mt.teststat0.1110.0190.130
ss.maxT0.0000.0000.001
wapply0.0000.0010.002