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This page was generated on 2022-01-14 13:05:29 -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 nebbiolo2


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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:multtest.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings multtest_2.50.0.tar.gz
StartedAt: 2022-01-13 08:40:24 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 08:41:25 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 60.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: multtest.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:multtest.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings multtest_2.50.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/multtest.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.50.0’
* 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:
  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-3.14-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 ‘/home/biocbuild/bbs-3.14-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-3.14-bioc/meat/multtest.Rcheck/00check.log’
for details.



Installation output

multtest.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL multtest
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘multtest’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c Rpack.c -o Rpack.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c VScount.c -o VScount.o
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c bootloop.c -o bootloop.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c mt.c -o mt.o
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c random.c -o random.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DUSEDOUBLE -fpic  -g -O2  -Wall -c sampling.c -o sampling.o
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-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]
  703 |   fscanf(fh, "%s", pdata->name);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stat_func.c:705:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  705 |     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]
  710 |     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]
  714 |       fscanf(fh, "%lg",&ftemp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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
EBMTP0.1540.0320.186
Hsets0.1710.0000.172
MTP-class000
MTP0.4420.0000.442
boot.null0.0260.0000.027
corr.null0.0160.0000.017
fwer2gfwer1.8670.0041.872
get.index0.2280.0040.233
meanX0.0080.0000.008
mt.maxT3.0550.0123.066
mt.plot0.2720.0000.273
mt.rawp2adjp0.2450.0000.245
mt.reject0.2350.0110.246
mt.sample.teststat0.1130.0000.113
mt.teststat0.1970.0120.209
ss.maxT000
wapply0.0010.0000.000