Yuzhou Chang
| Snapshot Date: 2023-11-03 14:00:11 -0400 (Fri, 03 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/IRISFGM |
| git_branch: devel |
| git_last_commit: f77bd35 |
| git_last_commit_date: 2023-10-24 11:30:04 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2023-11-04 11:37:56 -0400 (Sat, 04 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | R Under development (unstable) (2023-10-22 r85388) -- "Unsuffered Consequences" | 4593 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-10-23 r85389 ucrt) -- "Unsuffered Consequences" | 4347 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2023-10-31 r85450) -- "Unsuffered Consequences" | 4293 |
| 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 1026/2221 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IRISFGM 1.11.0 (landing page) Yuzhou Chang
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the IRISFGM package: - 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 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. |
| Package: IRISFGM |
| Version: 1.11.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IRISFGM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IRISFGM_1.11.0.tar.gz |
| StartedAt: 2023-11-04 02:47:27 -0400 (Sat, 04 Nov 2023) |
| EndedAt: 2023-11-04 03:12:37 -0400 (Sat, 04 Nov 2023) |
| EllapsedTime: 1509.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: IRISFGM.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IRISFGM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IRISFGM_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/IRISFGM.Rcheck’
* using R Under development (unstable) (2023-10-31 r85450)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRISFGM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IRISFGM’ version ‘1.11.0’
* 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:882:43: warning: format specifies type 'int' but the argument has type 'std::__vector_base<unsigned long, std::allocator<unsigned long>>::value_type' (aka 'unsigned long') [-Wformat]
read_array.cpp:1376:43: warning: format specifies type 'int' but the argument has type 'std::__vector_base<unsigned long, std::allocator<unsigned long>>::value_type' (aka 'unsigned long') [-Wformat]
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/IRISFGM.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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 8.934 0.384 11.942
RunBicluster 9.141 0.144 12.796
RunLTMG 8.572 0.184 11.364
RunDimensionReduction 6.969 0.064 9.339
* 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/IRISFGM.Rcheck/00check.log’
for details.
IRISFGM.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IRISFGM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘IRISFGM’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -DVER=2.08 -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -DVER=2.08 -fPIC -falign-functions=64 -Wall -g -O2 -c cluster.cpp -o cluster.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -DVER=2.08 -fPIC -falign-functions=64 -Wall -g -O2 -c expand.cpp -o expand.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -DVER=2.08 -fPIC -falign-functions=64 -Wall -g -O2 -c get_options.cpp -o get_options.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c getline.c -o getline.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -DVER=2.08 -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -DVER=2.08 -fPIC -falign-functions=64 -Wall -g -O2 -c make_graph.cpp -o make_graph.o
make_graph.cpp:51:5: warning: variable 'i' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
i++;
^
make_graph.cpp:45:29: note: incremented here
for (int i = 0; i < cols; i++) {
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -DVER=2.08 -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_irisfgm.cpp -o rcpp_irisfgm.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -DVER=2.08 -fPIC -falign-functions=64 -Wall -g -O2 -c read_array.cpp -o read_array.o
read_array.cpp:882:43: warning: format specifies type 'int' but the argument has type 'std::__vector_base<unsigned long, std::allocator<unsigned long>>::value_type' (aka 'unsigned long') [-Wformat]
fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
~~ ^~~~~~~~~~~~~
%lu
read_array.cpp:1376:43: warning: format specifies type 'int' but the argument has type 'std::__vector_base<unsigned long, std::allocator<unsigned long>>::value_type' (aka 'unsigned long') [-Wformat]
fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
~~ ^~~~~~~~~~~~~
%lu
2 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -DVER=2.08 -fPIC -falign-functions=64 -Wall -g -O2 -c struct.cpp -o struct.o
struct.cpp:75:15: warning: variable 'lastTime' set but not used [-Wunused-but-set-variable]
static long lastTime = 0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -DVER=2.08 -fPIC -falign-functions=64 -Wall -g -O2 -c write_block.cpp -o write_block.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 | 0.007 | 0.002 | 0.012 | |
| CalBinaryMultiSignal | 2.132 | 0.052 | 2.958 | |
| CalBinarySingleSignal | 0.488 | 0.014 | 0.673 | |
| CreateIRISFGMObject | 0.003 | 0.000 | 0.007 | |
| DotPlotPathway | 0.488 | 0.009 | 0.646 | |
| FindClassBasedOnMC | 8.934 | 0.384 | 11.942 | |
| FindGlobalMarkers | 1.993 | 0.046 | 2.627 | |
| FindMarker | 0.465 | 0.010 | 0.626 | |
| GetBinaryMultiSignal | 0.458 | 0.012 | 0.630 | |
| GetBinarySingleSignal | 0.477 | 0.008 | 0.646 | |
| GetLTMGmatrix | 0.526 | 0.011 | 0.705 | |
| PlotDimension | 0.985 | 0.016 | 1.300 | |
| PlotHeatmap | 0.817 | 0.022 | 1.113 | |
| PlotMarkerHeatmap | 1.822 | 0.040 | 2.536 | |
| PlotMeta | 0.868 | 0.008 | 1.246 | |
| PlotModuleNetwork | 2.248 | 0.020 | 3.134 | |
| PlotNetwork | 1.338 | 0.019 | 1.853 | |
| ProcessData | 0.487 | 0.009 | 0.669 | |
| RunBicluster | 9.141 | 0.144 | 12.796 | |
| RunClassification | 0.918 | 0.018 | 1.246 | |
| RunDimensionReduction | 6.969 | 0.064 | 9.339 | |
| RunDiscretization | 0.452 | 0.013 | 0.629 | |
| RunLTMG | 8.572 | 0.184 | 11.364 | |
| RunPathway | 0.425 | 0.007 | 0.562 | |
| SubsetData | 0.442 | 0.007 | 0.576 | |
| getMeta | 0.420 | 0.007 | 0.540 | |