| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:35 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 981/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IRISFGM 1.7.0 (landing page) Yuzhou Chang
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
| Package: IRISFGM |
| Version: 1.7.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IRISFGM.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings IRISFGM_1.7.0.tar.gz |
| StartedAt: 2022-12-29 00:45:17 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 00:50:41 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 323.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: IRISFGM.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IRISFGM.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings IRISFGM_1.7.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/IRISFGM.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'IRISFGM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IRISFGM' version '1.7.0'
* 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 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 long unsigned int>, long long unsigned int>::value_type' {aka 'long 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 long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=]
See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/IRISFGM.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/IRISFGM/libs/x64/IRISFGM.dll':
Found '_assert', possibly from 'assert' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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 nor [v]sprintf. 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, 1 NOTE
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/IRISFGM.Rcheck/00check.log'
for details.
IRISFGM.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL IRISFGM
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'IRISFGM' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cluster.cpp -o cluster.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c expand.cpp -o expand.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c get_options.cpp -o get_options.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getline.c -o getline.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main.cpp -o main.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c make_graph.cpp -o make_graph.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_irisfgm.cpp -o rcpp_irisfgm.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=]
882 | fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
| ~^
| |
| int
| %lld
read_array.cpp:883:35: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long 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 long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=]
1376 | fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
| ~^
| |
| int
| %lld
read_array.cpp:1377:35: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
1377 | for (std::size_t j = 0; j < cols; j++) {
| ~~^~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c write_block.cpp -o write_block.o
g++ -shared -s -static-libgcc -o IRISFGM.dll tmp.def 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 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-IRISFGM/00new/IRISFGM/libs/x64
** 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
** 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 | 0 | 0 | |
| CalBinaryMultiSignal | 0.42 | 0.08 | 0.50 | |
| CalBinarySingleSignal | 0.20 | 0.03 | 0.24 | |
| CreateIRISFGMObject | 0 | 0 | 0 | |
| DotPlotPathway | 0.20 | 0.02 | 0.21 | |
| FindClassBasedOnMC | 3.55 | 0.09 | 3.65 | |
| FindGlobalMarkers | 0.80 | 0.08 | 0.87 | |
| FindMarker | 0.20 | 0.03 | 0.23 | |
| GetBinaryMultiSignal | 0.19 | 0.03 | 0.22 | |
| GetBinarySingleSignal | 0.23 | 0.06 | 0.30 | |
| GetLTMGmatrix | 0.28 | 0.01 | 0.29 | |
| PlotDimension | 0.47 | 0.02 | 0.49 | |
| PlotHeatmap | 0.38 | 0.03 | 0.40 | |
| PlotMarkerHeatmap | 0.53 | 0.05 | 0.58 | |
| PlotMeta | 0.28 | 0.01 | 0.30 | |
| PlotModuleNetwork | 0.88 | 0.14 | 1.01 | |
| PlotNetwork | 1.28 | 0.04 | 1.32 | |
| ProcessData | 0.17 | 0.03 | 0.22 | |
| RunBicluster | 2.89 | 0.03 | 2.92 | |
| RunClassification | 0.47 | 0.03 | 0.50 | |
| RunDimensionReduction | 4.03 | 0.05 | 4.09 | |
| RunDiscretization | 0.17 | 0.04 | 0.22 | |
| RunLTMG | 2.69 | 0.07 | 2.75 | |
| RunPathway | 0.19 | 0.04 | 0.23 | |
| SubsetData | 0.18 | 0.03 | 0.22 | |
| getMeta | 0.18 | 0.07 | 0.23 | |