| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-02-27 02:34:36 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| 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 | ||||
|
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 985/2169 | 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: 2023-02-24 13:03:07 -0000 (Fri, 24 Feb 2023) |
| EndedAt: 2023-02-24 13:11:40 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 512.8 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 6.368 0.069 6.436
RunDimensionReduction 5.562 0.072 5.634
RunBicluster 5.273 0.104 5.378
RunLTMG 5.076 0.044 5.120
* 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 | 0.000 | 0.005 | |
| CalBinaryMultiSignal | 0.484 | 0.014 | 0.498 | |
| CalBinarySingleSignal | 0.456 | 0.000 | 0.456 | |
| CreateIRISFGMObject | 0.003 | 0.000 | 0.004 | |
| DotPlotPathway | 0.305 | 0.007 | 0.313 | |
| FindClassBasedOnMC | 6.368 | 0.069 | 6.436 | |
| FindGlobalMarkers | 0.987 | 0.003 | 0.990 | |
| FindMarker | 0.279 | 0.008 | 0.287 | |
| GetBinaryMultiSignal | 0.271 | 0.000 | 0.271 | |
| GetBinarySingleSignal | 0.264 | 0.008 | 0.272 | |
| GetLTMGmatrix | 0.279 | 0.008 | 0.287 | |
| PlotDimension | 0.611 | 0.008 | 0.619 | |
| PlotHeatmap | 0.456 | 0.004 | 0.460 | |
| PlotMarkerHeatmap | 0.936 | 0.016 | 0.952 | |
| PlotMeta | 0.502 | 0.011 | 0.514 | |
| PlotModuleNetwork | 2.745 | 0.120 | 2.865 | |
| PlotNetwork | 0.862 | 0.008 | 0.871 | |
| ProcessData | 0.286 | 0.000 | 0.286 | |
| RunBicluster | 5.273 | 0.104 | 5.378 | |
| RunClassification | 0.763 | 0.008 | 0.771 | |
| RunDimensionReduction | 5.562 | 0.072 | 5.634 | |
| RunDiscretization | 0.288 | 0.000 | 0.287 | |
| RunLTMG | 5.076 | 0.044 | 5.120 | |
| RunPathway | 0.284 | 0.004 | 0.287 | |
| SubsetData | 0.332 | 0.000 | 0.332 | |
| getMeta | 0.288 | 0.000 | 0.287 | |