Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:42 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 806/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GraphAlignment 1.56.0 (landing page) Joern P. Meier
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: GraphAlignment |
Version: 1.56.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GraphAlignment.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GraphAlignment_1.56.0.tar.gz |
StartedAt: 2021-10-14 10:05:10 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:05:24 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 14.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GraphAlignment.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GraphAlignment.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GraphAlignment_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/GraphAlignment.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GraphAlignment/DESCRIPTION’ ... OK * this is package ‘GraphAlignment’ version ‘1.56.0’ * 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-3.13-bioc/meat/GraphAlignment.Rcheck/00install.out’ for details. * 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 ‘/home/biocbuild/bbs-3.13-bioc/R/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. 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 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 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/GraphAlignment.Rcheck/00check.log’ for details.
GraphAlignment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL GraphAlignment ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘GraphAlignment’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c GA_alloc.c -o GA_alloc.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c GA_matrix.c -o GA_matrix.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c GA_matrix_R.c -o GA_matrix_R.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c GA_message.c -o GA_message.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c GA_vector.c -o GA_vector.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -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-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -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-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -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:64:30: warning: ‘last’ may be used uninitialized in this function [-Wmaybe-uninitialized] 64 | col j, j1, j2, endofpath, last, low, up, *collist, *matches; | ^~~~ gcc -shared -L/home/biocbuild/bbs-3.13-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-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/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)
GraphAlignment.Rcheck/GraphAlignment-Ex.timings
name | user | system | elapsed | |
AlignNetworks | 0.022 | 0.000 | 0.022 | |
AlignedPairs | 0.013 | 0.008 | 0.021 | |
AnalyzeAlignment | 0.022 | 0.000 | 0.023 | |
ComputeLinkParameters | 0.012 | 0.000 | 0.012 | |
ComputeM | 0.006 | 0.008 | 0.015 | |
ComputeNodeParameters | 0.002 | 0.000 | 0.002 | |
ComputeScores | 0.020 | 0.004 | 0.025 | |
CreateScoreMatrix | 0.000 | 0.004 | 0.004 | |
EncodeDirectedGraph | 0 | 0 | 0 | |
GenerateExample | 0.096 | 0.012 | 0.107 | |
GetBinNumber | 0.001 | 0.000 | 0.000 | |
InitialAlignment | 0.000 | 0.001 | 0.001 | |
InvertPermutation | 0.001 | 0.000 | 0.001 | |
LinearAssignment | 0.000 | 0.001 | 0.001 | |
MatrixToBin | 0.000 | 0.001 | 0.001 | |
Permute | 0.000 | 0.002 | 0.002 | |
Trace | 0.001 | 0.000 | 0.001 | |
VectorToBin | 0.001 | 0.000 | 0.001 | |