Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:43 -0400 (Fri, 15 Oct 2021).
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? 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 943/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IRISFGM 1.0.0 (landing page) Yuzhou Chang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: IRISFGM |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:IRISFGM.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings IRISFGM_1.0.0.tar.gz |
StartedAt: 2021-10-14 10:18:18 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:23:47 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 328.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IRISFGM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:IRISFGM.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings IRISFGM_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/IRISFGM.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 ‘IRISFGM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘IRISFGM’ version ‘1.0.0’ * 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 ... OK * 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 * 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 NOTE See ‘/home/biocbuild/bbs-3.13-bioc/meat/IRISFGM.Rcheck/00check.log’ for details.
IRISFGM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL IRISFGM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘IRISFGM’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-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-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-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 | 0.005 | 0.000 | 0.004 | |
CalBinaryMultiSignal | 1.173 | 0.016 | 1.188 | |
CalBinarySingleSignal | 0.215 | 0.004 | 0.219 | |
CreateIRISFGMObject | 0.001 | 0.000 | 0.002 | |
DotPlotPathway | 0.212 | 0.000 | 0.212 | |
FindClassBasedOnMC | 2.882 | 0.068 | 2.950 | |
FindGlobalMarkers | 1.096 | 0.011 | 1.108 | |
FindMarker | 0.212 | 0.008 | 0.220 | |
GetBinaryMultiSignal | 0.202 | 0.000 | 0.203 | |
GetBinarySingleSignal | 0.201 | 0.004 | 0.205 | |
GetLTMGmatrix | 0.179 | 0.004 | 0.184 | |
PlotDimension | 1.162 | 0.012 | 1.174 | |
PlotHeatmap | 0.290 | 0.004 | 0.294 | |
PlotMarkerHeatmap | 0.854 | 0.032 | 0.887 | |
PlotMeta | 0.279 | 0.040 | 0.318 | |
PlotModuleNetwork | 1.119 | 0.012 | 1.132 | |
PlotNetwork | 0.555 | 0.007 | 0.563 | |
ProcessData | 0.215 | 0.016 | 0.231 | |
RunBicluster | 3.716 | 0.056 | 3.773 | |
RunClassification | 0.472 | 0.008 | 0.481 | |
RunDimensionReduction | 4.71 | 0.04 | 4.75 | |
RunDiscretization | 0.206 | 0.003 | 0.209 | |
RunLTMG | 2.671 | 0.076 | 2.747 | |
RunPathway | 0.218 | 0.000 | 0.219 | |
SubsetData | 0.203 | 0.008 | 0.211 | |
getMeta | 0.203 | 0.000 | 0.203 | |