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CHECK report for AMOUNTAIN on merida1

This page was generated on 2020-08-11 11:59:12 -0400 (Tue, 11 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE AMOUNTAIN PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 49/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AMOUNTAIN 1.15.0
Dong Li
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/AMOUNTAIN
Branch: master
Last Commit: 6e77341
Last Changed Date: 2020-04-27 14:59:13 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AMOUNTAIN
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AMOUNTAIN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AMOUNTAIN_1.15.0.tar.gz
StartedAt: 2020-08-11 02:24:35 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 02:25:04 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 28.4 seconds
RetCode: 0
Status:  OK 
CheckDir: AMOUNTAIN.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AMOUNTAIN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AMOUNTAIN_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/AMOUNTAIN.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AMOUNTAIN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AMOUNTAIN’ version ‘1.15.0’
* 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 ‘AMOUNTAIN’ can be installed ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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/4.0/Resources/library/AMOUNTAIN/libs/AMOUNTAIN.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (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 installed files from ‘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 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/AMOUNTAIN.Rcheck/00check.log’
for details.



Installation output

AMOUNTAIN.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AMOUNTAIN
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘AMOUNTAIN’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  `gsl-config --cflags` -DR_DIRICHLETMULTINOMIAL -fPIC  -Wall -g -O2  -c AMOUNTAIN.c -o AMOUNTAIN.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 AMOUNTAIN.so AMOUNTAIN.o -L/usr/local/lib -lgsl -lgslcblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-AMOUNTAIN/00new/AMOUNTAIN/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘AMOUNTAIN.Rmd’ using ‘UTF-8’ 
** 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 (AMOUNTAIN)

Tests output


Example timings

AMOUNTAIN.Rcheck/AMOUNTAIN-Ex.timings

nameusersystemelapsed
CGPFixSS0.0040.0010.006
CGPFixSSMultiLayer0.0110.0010.011
CGPFixSSTwolayer0.0050.0010.006
EuclideanProjectionENNORM0.0010.0000.002
moduleIdentificationGPFixSS0.0090.0020.011
moduleIdentificationGPFixSSMultilayer0.0120.0020.014
moduleIdentificationGPFixSSTwolayer0.0210.0050.025
multilayernetworkSimulation0.0010.0010.002
networkSimulation0.0010.0010.001
twolayernetworkSimulation0.0030.0020.005