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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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

Package 895/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GraphAlignment 1.71.0  (landing page)
Joern P. Meier
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/GraphAlignment
git_branch: devel
git_last_commit: 3faa9a6
git_last_commit_date: 2024-10-29 09:28:35 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for GraphAlignment on nebbiolo1

To the developers/maintainers of the GraphAlignment package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GraphAlignment
Version: 1.71.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GraphAlignment.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GraphAlignment_1.71.0.tar.gz
StartedAt: 2024-12-23 22:37:47 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 22:38:06 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 19.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GraphAlignment.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GraphAlignment.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GraphAlignment_1.71.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GraphAlignment.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GraphAlignment/DESCRIPTION’ ... OK
* this is package ‘GraphAlignment’ version ‘1.71.0’
* 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 ... WARNING
Found the following significant warnings:
  lap.c:348:9: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  lap.c:358:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  lap.c:371:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  lap.c:384:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  lap.c:394:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/GraphAlignment.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 code 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 whether startup messages can be suppressed ... 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 ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/GraphAlignment/libs/GraphAlignment.so’:
  Found ‘__printf_chk’, 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 nor [v]sprintf. 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 ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/GraphAlignment.Rcheck/00check.log’
for details.


Installation output

GraphAlignment.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GraphAlignment
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘GraphAlignment’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c GA_alloc.c -o GA_alloc.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c GA_matrix.c -o GA_matrix.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c GA_matrix_R.c -o GA_matrix_R.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c GA_message.c -o GA_message.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c GA_vector.c -o GA_vector.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -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]
  139 |     int size = LENGTH(robj);
      |         ^~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -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]
  138 |                 if (matrix->elts[i][j] == 1)
      |                    ^
GraphAlignment.c:159:20: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
  159 |                 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]
  264 |     int size = LENGTH(robj);
      |         ^~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c lap.c -o lap.o
lap.c: In function ‘LAP_checklap’:
lap.c:348:9: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  348 |         scanf("%c", &wait);
      |         ^~~~~~~~~~~~~~~~~~
lap.c:358:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  358 |       scanf("%c", &wait);
      |       ^~~~~~~~~~~~~~~~~~
lap.c:371:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  371 |       scanf("%c", &wait);
      |       ^~~~~~~~~~~~~~~~~~
lap.c:384:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  384 |       scanf("%c", &wait);
      |       ^~~~~~~~~~~~~~~~~~
lap.c:394:7: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  394 |       scanf("%c", &wait);
      |       ^~~~~~~~~~~~~~~~~~
lap.c: In function ‘LAP_lap’:
lap.c:260:11: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized]
  260 |         h = assigncost[i][j1] - v[j1] - min;
      |         ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
lap.c:65:8: note: ‘min’ was declared here
   65 |   cost min, h, umin, usubmin, v2, *d;
      |        ^~~
lap.c:293:19: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized]
  293 |     for (k = 0; k <= last; k++)
      |                 ~~^~~~~~~
lap.c:64:30: note: ‘last’ was declared here
   64 |   col  j, j1, j2, endofpath, last, low, up, *collist, *matches;
      |                              ^~~~
gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/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 -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-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
AlignNetworks0.0160.0080.024
AlignedPairs0.0180.0000.018
AnalyzeAlignment0.0220.0010.022
ComputeLinkParameters0.0030.0010.004
ComputeM0.0040.0060.012
ComputeNodeParameters0.0020.0000.002
ComputeScores0.0230.0010.023
CreateScoreMatrix0.0010.0030.003
EncodeDirectedGraph000
GenerateExample0.0970.0070.106
GetBinNumber0.0000.0000.001
InitialAlignment0.0010.0010.001
InvertPermutation000
LinearAssignment0.0000.0000.001
MatrixToBin0.0000.0000.001
Permute0.0000.0010.002
Trace000
VectorToBin0.0010.0000.000