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CHECK report for GraphAlignment on celaya2

This page was generated on 2020-01-16 13:31:09 -0500 (Thu, 16 Jan 2020).

Package 739/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GraphAlignment 1.51.0
Joern P. Meier
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/GraphAlignment
Branch: master
Last Commit: c8eed71
Last Changed Date: 2019-10-29 13:34:48 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GraphAlignment
Version: 1.51.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GraphAlignment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GraphAlignment_1.51.0.tar.gz
StartedAt: 2020-01-16 05:10:33 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 05:11:07 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 34.3 seconds
RetCode: 0
Status:  OK 
CheckDir: GraphAlignment.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GraphAlignment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GraphAlignment_1.51.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GraphAlignment.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GraphAlignment/DESCRIPTION’ ... OK
* this is package ‘GraphAlignment’ version ‘1.51.0’
* 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 ‘GraphAlignment’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
File ‘GraphAlignment/R/GraphAlignment.R’:
  .Last.lib calls:
    library.dynam.unload("GraphAlignment", libpath)

Package detach functions should not call ‘library.dynam.unload’.
See section ‘Good practice’ in '?.Last.lib'.

AlignNetworks: no visible global function definition for ‘rnorm’
GenerateExample: no visible global function definition for ‘runif’
GenerateExample: no visible global function definition for ‘rnorm’
GenerateExample: no visible global function definition for ‘pnorm’
InitialAlignment: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  pnorm rnorm runif
Consider adding
  importFrom("stats", "pnorm", "rnorm", "runif")
to your NAMESPACE file.
* 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/GraphAlignment/libs/GraphAlignment.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘GraphAlignment.pdf’ from 417Kb to 311Kb
  consider running tools::compactPDF() on these files
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/GraphAlignment.Rcheck/00check.log’
for details.



Installation output

GraphAlignment.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GraphAlignment
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘GraphAlignment’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c GA_alloc.c -o GA_alloc.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c GA_matrix.c -o GA_matrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c GA_matrix_R.c -o GA_matrix_R.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c GA_message.c -o GA_message.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c GA_vector.c -o GA_vector.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c:139:9: warning: unused variable 'size' [-Wunused-variable]
    int size = LENGTH(robj);
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c:143:23: warning: add explicit braces to avoid dangling else [-Wdangling-else]
                    } else
                      ^
GraphAlignment.c:164:23: warning: add explicit braces to avoid dangling else [-Wdangling-else]
                    } else
                      ^
GraphAlignment.c:264:9: warning: unused variable 'size' [-Wunused-variable]
    int size = LENGTH(robj);
        ^
3 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c lap.c -o lap.o
clang -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 GraphAlignment.so GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-GraphAlignment/00new/GraphAlignment/libs
** R
** 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 (GraphAlignment)

Tests output


Example timings

GraphAlignment.Rcheck/GraphAlignment-Ex.timings

nameusersystemelapsed
AlignNetworks0.0480.0100.059
AlignedPairs0.0280.0080.035
AnalyzeAlignment0.0310.0030.033
ComputeLinkParameters0.0040.0010.005
ComputeM0.0120.0070.018
ComputeNodeParameters0.0020.0000.004
ComputeScores0.0500.0090.059
CreateScoreMatrix0.0030.0030.007
EncodeDirectedGraph0.0000.0000.001
GenerateExample0.1400.0250.168
GetBinNumber0.0000.0000.001
InitialAlignment0.0010.0000.001
InvertPermutation0.0010.0010.001
LinearAssignment0.0000.0000.001
MatrixToBin0.0010.0000.002
Permute0.0020.0010.003
Trace0.0010.0000.000
VectorToBin0.0000.0000.001