Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:43 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the IRISFGM package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IRISFGM.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. |
Package 986/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IRISFGM 1.7.0 (landing page) Yuzhou Chang
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
Package: IRISFGM |
Version: 1.7.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:IRISFGM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings IRISFGM_1.7.0.tar.gz |
StartedAt: 2023-02-28 06:32:46 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 06:41:14 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 507.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: IRISFGM.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:IRISFGM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings IRISFGM_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/IRISFGM.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘IRISFGM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘IRISFGM’ version ‘1.7.0’ * package encoding: UTF-8 * 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 ‘IRISFGM’ can be installed ... WARNING Found the following significant warnings: read_array.cpp:882:26: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] read_array.cpp:1376:26: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] See ‘/home/biocbuild/bbs-3.17-bioc/meat/IRISFGM.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 ... OK * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed FindClassBasedOnMC 7.295 0.300 7.595 RunDimensionReduction 5.618 0.124 5.742 RunBicluster 5.414 0.135 5.550 RunLTMG 5.119 0.052 5.172 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘IRISFGM_Rpackage.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/IRISFGM.Rcheck/00check.log’ for details.
IRISFGM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL IRISFGM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘IRISFGM’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fopenmp -DVER=2.08 -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fopenmp -DVER=2.08 -fPIC -g -O2 -Wall -c cluster.cpp -o cluster.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fopenmp -DVER=2.08 -fPIC -g -O2 -Wall -c expand.cpp -o expand.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fopenmp -DVER=2.08 -fPIC -g -O2 -Wall -c get_options.cpp -o get_options.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c getline.c -o getline.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fopenmp -DVER=2.08 -fPIC -g -O2 -Wall -c main.cpp -o main.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fopenmp -DVER=2.08 -fPIC -g -O2 -Wall -c make_graph.cpp -o make_graph.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fopenmp -DVER=2.08 -fPIC -g -O2 -Wall -c rcpp_irisfgm.cpp -o rcpp_irisfgm.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fopenmp -DVER=2.08 -fPIC -g -O2 -Wall -c read_array.cpp -o read_array.o read_array.cpp: In function ‘void discretize_new(const char*)’: read_array.cpp:882:26: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] 882 | fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]); | ~^ | | | int | %ld read_array.cpp:883:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 883 | for (std::size_t j = 0; j < cols; j++) { | ~~^~~~~~ read_array.cpp: In function ‘void discretize_rpkm(const char*)’: read_array.cpp:1376:26: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wformat=] 1376 | fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]); | ~^ | | | int | %ld read_array.cpp:1377:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1377 | for (std::size_t j = 0; j < cols; j++) { | ~~^~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fopenmp -DVER=2.08 -fPIC -g -O2 -Wall -c struct.cpp -o struct.o struct.cpp: In function ‘void uglyTime(const char*, ...)’: struct.cpp:75:15: warning: variable ‘lastTime’ set but not used [-Wunused-but-set-variable] 75 | static long lastTime = 0; | ^~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include -fopenmp -DVER=2.08 -fPIC -g -O2 -Wall -c write_block.cpp -o write_block.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o IRISFGM.so RcppExports.o cluster.o expand.o get_options.o getline.o main.o make_graph.o rcpp_irisfgm.o read_array.o struct.o write_block.o -fopenmp -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-IRISFGM/00new/IRISFGM/libs ** R ** data ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘ReadFrom10X_h5’ in package ‘IRISFGM’ Creating a generic function from function ‘ReadFrom10X_folder’ in package ‘IRISFGM’ ** 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 (IRISFGM)
IRISFGM.Rcheck/IRISFGM-Ex.timings
name | user | system | elapsed | |
AddMeta | 0.006 | 0.001 | 0.006 | |
CalBinaryMultiSignal | 0.493 | 0.015 | 0.508 | |
CalBinarySingleSignal | 0.429 | 0.005 | 0.433 | |
CreateIRISFGMObject | 0.000 | 0.004 | 0.004 | |
DotPlotPathway | 0.279 | 0.007 | 0.288 | |
FindClassBasedOnMC | 7.295 | 0.300 | 7.595 | |
FindGlobalMarkers | 1.049 | 0.020 | 1.069 | |
FindMarker | 0.295 | 0.000 | 0.296 | |
GetBinaryMultiSignal | 0.286 | 0.007 | 0.294 | |
GetBinarySingleSignal | 0.293 | 0.005 | 0.297 | |
GetLTMGmatrix | 0.285 | 0.007 | 0.293 | |
PlotDimension | 0.606 | 0.001 | 0.606 | |
PlotHeatmap | 0.519 | 0.028 | 0.547 | |
PlotMarkerHeatmap | 0.882 | 0.007 | 0.889 | |
PlotMeta | 0.527 | 0.008 | 0.535 | |
PlotModuleNetwork | 1.653 | 0.068 | 1.720 | |
PlotNetwork | 0.922 | 0.011 | 0.934 | |
ProcessData | 0.292 | 0.000 | 0.293 | |
RunBicluster | 5.414 | 0.135 | 5.550 | |
RunClassification | 0.714 | 0.000 | 0.715 | |
RunDimensionReduction | 5.618 | 0.124 | 5.742 | |
RunDiscretization | 0.289 | 0.000 | 0.289 | |
RunLTMG | 5.119 | 0.052 | 5.172 | |
RunPathway | 0.286 | 0.000 | 0.287 | |
SubsetData | 0.326 | 0.000 | 0.326 | |
getMeta | 0.282 | 0.008 | 0.290 | |