Vladimir Kiselev
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/SC3 |
| Branch: RELEASE_3_9 |
| Last Commit: cdcc29c |
| Last Changed Date: 2019-05-02 11:53:59 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:34:47 -0400 (Wed, 16 Oct 2019).
| Package 1457/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SC3 1.12.0 Vladimir Kiselev
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SC3 |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SC3.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SC3_1.12.0.tar.gz |
| StartedAt: 2019-10-16 06:54:12 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:58:15 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 242.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SC3.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SC3.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SC3_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SC3.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'SC3/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SC3' version '1.12.0' * 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 'SC3' 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SC3/libs/i386/SC3.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SC3/libs/x64/SC3.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) 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. 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SC3.Rcheck/00check.log' for details.
SC3.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SC3_1.12.0.tar.gz && rm -rf SC3.buildbin-libdir && mkdir SC3.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SC3.buildbin-libdir SC3_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SC3_1.12.0.zip && rm SC3_1.12.0.tar.gz SC3_1.12.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1726k 100 1726k 0 0 20.1M 0 --:--:-- --:--:-- --:--:-- 21.9M
install for i386
* installing *source* package 'SC3' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cppFunctions.cpp -o cppFunctions.o
cppFunctions.cpp: In function 'arma::mat consmx(arma::mat)':
cppFunctions.cpp:63:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j < dat.n_cols; j++) {
^
cppFunctions.cpp:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < dat.n_rows; i++) {
^
cppFunctions.cpp:65:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (k = i + 1; k < dat.n_rows; k++) {
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o SC3.dll tmp.def RcppExports.o cppFunctions.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/SC3.buildbin-libdir/00LOCK-SC3/00new/SC3/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SC3'
finding HTML links ... done
ED1 html
ED2 html
ann html
calculate_distance html
calculate_stability html
consensus_matrix html
consmx html
estkTW html
get_auroc html
get_biolgy html
get_de_genes html
get_marker_genes html
get_outl_cells html
get_processed_dataset html
markers_for_heatmap html
norm_laplacian html
organise_de_genes html
organise_marker_genes html
prepare_for_svm html
reindex_clusters html
sc3 html
sc3_calc_biology html
sc3_calc_consens html
sc3_calc_dists html
sc3_calc_transfs html
sc3_estimate_k html
sc3_export_results_xls html
sc3_interactive html
sc3_kmeans html
sc3_plot_cluster_stability html
sc3_plot_consensus html
sc3_plot_de_genes html
sc3_plot_expression html
sc3_plot_markers html
sc3_plot_silhouette html
sc3_prepare html
sc3_run_svm html
support_vector_machines html
tmult html
transformation html
yan html
** 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
install for x64
* installing *source* package 'SC3' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cppFunctions.cpp -o cppFunctions.o
cppFunctions.cpp: In function 'arma::mat consmx(arma::mat)':
cppFunctions.cpp:63:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (j = 0; j < dat.n_cols; j++) {
^
cppFunctions.cpp:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < dat.n_rows; i++) {
^
cppFunctions.cpp:65:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (k = i + 1; k < dat.n_rows; k++) {
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o SC3.dll tmp.def RcppExports.o cppFunctions.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/SC3.buildbin-libdir/SC3/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SC3' as SC3_1.12.0.zip
* DONE (SC3)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SC3' successfully unpacked and MD5 sums checked
|
SC3.Rcheck/examples_i386/SC3-Ex.timings
|
SC3.Rcheck/examples_x64/SC3-Ex.timings
|