Package: GraphAlignment

Version: 1.42.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GraphAlignment_1.42.0.tar.gz

StartedAt: 2018-04-12 04:45:36 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 04:45:59 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 22.7 seconds

RetCode: 0

Status:  OK

CheckDir: GraphAlignment.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GraphAlignment_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/GraphAlignment.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.42.0’
* 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 loading without being on the library search path ... 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
File ‘GraphAlignment/libs/GraphAlignment.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Objects: ‘GA_message.o’, ‘lap.o’
  Found ‘_putchar’, possibly from ‘putchar’ (C)
    Object: ‘lap.o’

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.

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 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/GraphAlignment.Rcheck/00check.log’
for details.

* installing *source* package ‘GraphAlignment’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -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   -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   -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   -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   -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   -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   -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   -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 /Users/biocbuild/bbs-3.6-bioc/meat/GraphAlignment.Rcheck/GraphAlignment/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GraphAlignment)

name	user	system	elapsed
AlignNetworks	0.091	0.005	0.099
AlignedPairs	0.258	0.003	0.268
AnalyzeAlignment	0.041	0.002	0.042
ComputeLinkParameters	0.022	0.000	0.023
ComputeM	0.029	0.005	0.034
ComputeNodeParameters	0.007	0.000	0.007
ComputeScores	0.073	0.002	0.074
CreateScoreMatrix	0.004	0.002	0.006
EncodeDirectedGraph	0.001	0.001	0.001
GenerateExample	0.110	0.007	0.121
GetBinNumber	0.000	0.000	0.001
InitialAlignment	0.002	0.000	0.003
InvertPermutation	0.001	0.000	0.001
LinearAssignment	0.001	0.000	0.001
MatrixToBin	0.001	0.000	0.002
Permute	0.001	0.001	0.002
Trace	0.001	0.000	0.000
VectorToBin	0.002	0.000	0.001