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This page was generated on 2022-04-13 12:06:40 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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CHECK results for GraphAlignment on tokay2


To the developers/maintainers of the GraphAlignment package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GraphAlignment.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 819/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GraphAlignment 1.58.0  (landing page)
Joern P. Meier
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/GraphAlignment
git_branch: RELEASE_3_14
git_last_commit: bc70f85
git_last_commit_date: 2021-10-26 11:51:55 -0400 (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    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GraphAlignment
Version: 1.58.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GraphAlignment.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GraphAlignment_1.58.0.tar.gz
StartedAt: 2022-04-12 20:48:26 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 20:49:04 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 38.0 seconds
RetCode: 0
Status:   OK  
CheckDir: GraphAlignment.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GraphAlignment.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GraphAlignment_1.58.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GraphAlignment.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GraphAlignment/DESCRIPTION' ... OK
* this is package 'GraphAlignment' version '1.58.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/GraphAlignment/libs/i386/GraphAlignment.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/GraphAlignment/libs/x64/GraphAlignment.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GraphAlignment.Rcheck/00check.log'
for details.



Installation output

GraphAlignment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GraphAlignment_1.58.0.tar.gz && rm -rf GraphAlignment.buildbin-libdir && mkdir GraphAlignment.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GraphAlignment.buildbin-libdir GraphAlignment_1.58.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GraphAlignment_1.58.0.zip && rm GraphAlignment_1.58.0.tar.gz GraphAlignment_1.58.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  103k  100  103k    0     0   369k      0 --:--:-- --:--:-- --:--:--  371k

install for i386

* installing *source* package 'GraphAlignment' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GA_alloc.c -o GA_alloc.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GA_matrix.c -o GA_matrix.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GA_matrix_R.c -o GA_matrix_R.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GA_message.c -o GA_message.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GA_vector.c -o GA_vector.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c: In function 'GA_clamp_mode_from_R':
GA_vector_R.c:139:9: warning: unused variable 'size' [-Wunused-variable]
     int size = LENGTH(robj);
         ^~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c: In function 'GA_encode_directed_graph':
GraphAlignment.c:138:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
                 if (matrix->elts[i][j] == 1)
                    ^
GraphAlignment.c:159:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
                 if (matrix->elts[i][j] == 1)
                    ^
GraphAlignment.c: In function 'GA_directed_mode_from_R':
GraphAlignment.c:264:9: warning: unused variable 'size' [-Wunused-variable]
     int size = LENGTH(robj);
         ^~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c lap.c -o lap.o
lap.c: In function 'LAP_lap':
lap.c:64:30: warning: 'last' may be used uninitialized in this function [-Wmaybe-uninitialized]
   col  j, j1, j2, endofpath, last, low, up, *collist, *matches;
                              ^~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o GraphAlignment.dll tmp.def GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GraphAlignment.buildbin-libdir/00LOCK-GraphAlignment/00new/GraphAlignment/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GraphAlignment'
    finding HTML links ... done
    AlignNetworks                           html  
    AlignedPairs                            html  
    AnalyzeAlignment                        html  
    ComputeLinkParameters                   html  
    ComputeM                                html  
    ComputeNodeParameters                   html  
    ComputeScores                           html  
    CreateScoreMatrix                       html  
    EncodeDirectedGraph                     html  
    GenerateExample                         html  
    GetBinNumber                            html  
    InitialAlignment                        html  
    InvertPermutation                       html  
    LinearAssignment                        html  
    MatrixToBin                             html  
    Permute                                 html  
    Trace                                   html  
    VectorToBin                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GraphAlignment' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GA_alloc.c -o GA_alloc.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GA_matrix.c -o GA_matrix.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GA_matrix_R.c -o GA_matrix_R.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GA_message.c -o GA_message.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GA_vector.c -o GA_vector.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c: In function 'GA_clamp_mode_from_R':
GA_vector_R.c:139:9: warning: unused variable 'size' [-Wunused-variable]
     int size = LENGTH(robj);
         ^~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c: In function 'GA_encode_directed_graph':
GraphAlignment.c:138:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
                 if (matrix->elts[i][j] == 1)
                    ^
GraphAlignment.c:159:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
                 if (matrix->elts[i][j] == 1)
                    ^
GraphAlignment.c: In function 'GA_directed_mode_from_R':
GraphAlignment.c:264:9: warning: unused variable 'size' [-Wunused-variable]
     int size = LENGTH(robj);
         ^~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c lap.c -o lap.o
lap.c: In function 'LAP_lap':
lap.c:64:30: warning: 'last' may be used uninitialized in this function [-Wmaybe-uninitialized]
   col  j, j1, j2, endofpath, last, low, up, *collist, *matches;
                              ^~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o GraphAlignment.dll tmp.def GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GraphAlignment.buildbin-libdir/GraphAlignment/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GraphAlignment' as GraphAlignment_1.58.0.zip
* DONE (GraphAlignment)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GraphAlignment' successfully unpacked and MD5 sums checked

Tests output


Example timings

GraphAlignment.Rcheck/examples_i386/GraphAlignment-Ex.timings

nameusersystemelapsed
AlignNetworks0.040.000.05
AlignedPairs0.030.000.03
AnalyzeAlignment0.050.000.05
ComputeLinkParameters000
ComputeM0.010.000.02
ComputeNodeParameters000
ComputeScores0.050.000.04
CreateScoreMatrix000
EncodeDirectedGraph000
GenerateExample0.190.000.19
GetBinNumber000
InitialAlignment000
InvertPermutation000
LinearAssignment000
MatrixToBin000
Permute000
Trace000
VectorToBin000

GraphAlignment.Rcheck/examples_x64/GraphAlignment-Ex.timings

nameusersystemelapsed
AlignNetworks0.030.000.03
AlignedPairs0.030.020.05
AnalyzeAlignment0.050.000.05
ComputeLinkParameters000
ComputeM0.010.000.01
ComputeNodeParameters0.020.000.02
ComputeScores0.030.000.03
CreateScoreMatrix000
EncodeDirectedGraph000
GenerateExample0.170.000.17
GetBinNumber000
InitialAlignment000
InvertPermutation000
LinearAssignment000
MatrixToBin000
Permute000
Trace000
VectorToBin000