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This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 1339/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multtest 2.56.0  (landing page)
Katherine S. Pollard
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/multtest
git_branch: RELEASE_3_17
git_last_commit: 6199757
git_last_commit_date: 2023-04-25 09:38:25 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for multtest on kjohnson2


To the developers/maintainers of the multtest package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: multtest
Version: 2.56.0
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_2.56.0.tar.gz
StartedAt: 2023-10-18 10:31:54 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 10:34:14 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 139.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: multtest.Rcheck
Warnings: 4

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_2.56.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/multtest.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘multtest/DESCRIPTION’ ... OK
* this is package ‘multtest’ version ‘2.56.0’
* 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-3.17-bioc-mac-arm64/meat/multtest.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) mt.maxT.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) mt.maxT.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) mt.plot.Rd:37: Escaped LaTeX specials: \#
* 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/multtest/libs/multtest.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (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 nor [v]sprintf. 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
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
mt.maxT 4.341  0.087   6.803
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/multtest.Rcheck/00check.log’
for details.



Installation output

multtest.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘multtest’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DUSEDOUBLE -fPIC  -falign-functions=64 -Wall -g -O2  -c Rpack.c -o Rpack.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DUSEDOUBLE -fPIC  -falign-functions=64 -Wall -g -O2  -c VScount.c -o VScount.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DUSEDOUBLE -fPIC  -falign-functions=64 -Wall -g -O2  -c block_sampling_fixed.c -o block_sampling_fixed.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DUSEDOUBLE -fPIC  -falign-functions=64 -Wall -g -O2  -c bootloop.c -o bootloop.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DUSEDOUBLE -fPIC  -falign-functions=64 -Wall -g -O2  -c mt.c -o mt.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DUSEDOUBLE -fPIC  -falign-functions=64 -Wall -g -O2  -c pairt_sampling.c -o pairt_sampling.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DUSEDOUBLE -fPIC  -falign-functions=64 -Wall -g -O2  -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DUSEDOUBLE -fPIC  -falign-functions=64 -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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DUSEDOUBLE -fPIC  -falign-functions=64 -Wall -g -O2  -c sampling.c -o sampling.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DUSEDOUBLE -fPIC  -falign-functions=64 -Wall -g -O2  -c sampling_fixed.c -o sampling_fixed.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DUSEDOUBLE -fPIC  -falign-functions=64 -Wall -g -O2  -c stat_func.c -o stat_func.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DUSEDOUBLE -fPIC  -falign-functions=64 -Wall -g -O2  -c stat_order.c -o stat_order.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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-class0.0010.0000.001
EBMTP0.1750.0070.428
Hsets0.1980.0070.469
MTP-class000
MTP0.5480.0090.861
boot.null0.0260.0010.045
corr.null0.0200.0020.032
fwer2gfwer2.3270.0244.033
get.index0.2520.0090.400
meanX0.0110.0010.018
mt.maxT4.3410.0876.803
mt.plot0.5020.0200.793
mt.rawp2adjp0.4590.0130.731
mt.reject0.4560.0120.717
mt.sample.teststat0.1220.0120.198
mt.teststat0.1840.0170.337
ss.maxT000
wapply0.0010.0000.001