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This page was generated on 2022-01-14 13:08:14 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for multtest on machv2


To the developers/maintainers of the multtest package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/multtest.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1250/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multtest 2.50.0  (landing page)
Katherine S. Pollard
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/multtest
git_branch: RELEASE_3_14
git_last_commit: 1de9664
git_last_commit_date: 2021-10-26 11:45:35 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: multtest
Version: 2.50.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:multtest.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings multtest_2.50.0.tar.gz
StartedAt: 2022-01-13 15:37:59 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 15:39:52 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 112.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: multtest.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:multtest.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings multtest_2.50.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/multtest.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multtest/DESCRIPTION’ ... OK
* this is package ‘multtest’ version ‘2.50.0’
* 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:
  random.c:48:6: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
See ‘/Users/biocbuild/bbs-3.14-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 ‘clusterEvalQ’
EBMTP: no visible global function definition for ‘stopCluster’
MTP: no visible global function definition for ‘makeCluster’
MTP: no visible global function definition for ‘clusterEvalQ’
MTP: no visible global function definition for ‘stopCluster’
boot.null: no visible global function definition for ‘clusterApply’
boot.null: no visible global function definition for ‘clusterApplyLB’
EBupdate,EBMTP: no visible binding for global variable ‘y’
update,MTP: no visible binding for global variable ‘y’
Undefined global functions or variables:
  clusterApply clusterApplyLB clusterEvalQ makeCluster stopCluster y
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/multtest/libs/multtest.so’:
  Found ‘___stderrp’, 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/multtest.Rcheck/00check.log’
for details.



Installation output

multtest.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL multtest
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘multtest’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c Rpack.c -o Rpack.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c VScount.c -o VScount.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c block_sampling_fixed.c -o block_sampling_fixed.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c bootloop.c -o bootloop.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c mt.c -o mt.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c pairt_sampling.c -o pairt_sampling.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c random.c -o random.o
random.c:48:6: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
  z1=abs(seed); /*setting the seed to z1 and initialize it*/
     ^
random.c:48:6: note: use function 'labs' instead
  z1=abs(seed); /*setting the seed to z1 and initialize it*/
     ^~~
     labs
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c sampling.c -o sampling.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c sampling_fixed.c -o sampling_fixed.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c stat_func.c -o stat_func.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fPIC  -Wall -g -O2  -c stat_order.c -o stat_order.o
clang -mmacosx-version-min=10.13 -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 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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-class0.0000.0000.001
EBMTP0.3320.0260.357
Hsets0.3740.0110.387
MTP-class000
MTP1.0650.0171.124
boot.null0.0560.0030.059
corr.null0.0290.0050.033
fwer2gfwer4.4780.0144.495
get.index0.4520.0150.466
meanX0.0150.0010.017
mt.maxT4.8690.0534.925
mt.plot0.3790.0110.391
mt.rawp2adjp0.3340.0060.341
mt.reject0.3520.0090.361
mt.sample.teststat0.1510.0150.167
mt.teststat0.2240.0190.246
ss.maxT0.0000.0000.001
wapply0.0020.0000.002