Aaron Lun
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/batchelor |
| Branch: RELEASE_3_9 |
| Last Commit: a8ba15b |
| Last Changed Date: 2019-05-22 23:44:34 -0400 (Wed, 22 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:43:52 -0400 (Wed, 16 Oct 2019).
| Package 110/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| batchelor 1.0.1 Aaron Lun
| 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: batchelor |
| Version: 1.0.1 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/batchelor_1.0.1.tar.gz && rm -rf batchelor.buildbin-libdir && mkdir batchelor.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=batchelor.buildbin-libdir batchelor_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL batchelor_1.0.1.zip && rm batchelor_1.0.1.tar.gz batchelor_1.0.1.zip |
| StartedAt: 2019-10-15 21:07:06 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 21:09:41 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 155.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/batchelor_1.0.1.tar.gz && rm -rf batchelor.buildbin-libdir && mkdir batchelor.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=batchelor.buildbin-libdir batchelor_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL batchelor_1.0.1.zip && rm batchelor_1.0.1.tar.gz batchelor_1.0.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 86098 100 86098 0 0 1296k 0 --:--:-- --:--:-- --:--:-- 1449k
install for i386
* installing *source* package 'batchelor' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -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/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c adjust_shift_variance.cpp -o adjust_shift_variance.o
adjust_shift_variance.cpp: In function 'SEXPREC* adjust_shift_variance(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
adjust_shift_variance.cpp:131:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t other=0; other::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
cosine_norm.cpp:50:47: required from 'SEXPREC* cosine_norm_internal(SEXP, SEXP) [with M = beachmat::lin_matrix >; SEXP = SEXPREC*]'
cosine_norm.cpp:70:79: required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ref->get_nrow() > indices.size()) {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
cosine_norm.cpp:50:47: required from 'SEXPREC* cosine_norm_internal(SEXP, SEXP) [with M = beachmat::lin_matrix >; SEXP = SEXPREC*]'
cosine_norm.cpp:72:79: required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -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/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c find_mutual_nns.cpp -o find_mutual_nns.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -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/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -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/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c smooth_gaussian_kernel.cpp -o smooth_gaussian_kernel.o
smooth_gaussian_kernel.cpp: In function 'SEXPREC* smooth_gaussian_kernel(SEXP, SEXP, SEXP, SEXP)':
smooth_gaussian_kernel.cpp:20:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (npairs!=_index.size()) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -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/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c unlog_exprs.cpp -o unlog_exprs.o
unlog_exprs.cpp: In function 'SEXPREC* unlog_exprs_scaled(SEXP, SEXP, SEXP, SEXP, SEXP)':
unlog_exprs.cpp:51:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (slen!=rescaling.size()) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -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/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::IntegerVector check_subset_vector(SEXP, size_t)':
utils.cpp:9:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (isNA(s) || s < 0 || s >= len) {
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o batchelor.dll tmp.def adjust_shift_variance.o cosine_norm.o find_mutual_nns.o init.o smooth_gaussian_kernel.o unlog_exprs.o utils.o -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/batchelor.buildbin-libdir/00LOCK-batchelor/00new/batchelor/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'batchelor'
finding HTML links ... done
BatchelorParam html
finding level-2 HTML links ... done
batchCorrect html
checkInputs html
cosineNorm html
divideIntoBatches html
fastMNN html
findMutualNN html
mnnCorrect html
multiBatchNorm html
multiBatchPCA html
rescaleBatches 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 'batchelor' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -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/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c adjust_shift_variance.cpp -o adjust_shift_variance.o
adjust_shift_variance.cpp: In function 'SEXPREC* adjust_shift_variance(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
adjust_shift_variance.cpp:131:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t other=0; other::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
cosine_norm.cpp:50:47: required from 'SEXPREC* cosine_norm_internal(SEXP, SEXP) [with M = beachmat::lin_matrix >; SEXP = SEXPREC*]'
cosine_norm.cpp:70:79: required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (ref->get_nrow() > indices.size()) {
^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h: In instantiation of 'Rcpp::traits::storage_type<13>::type* beachmat::const_column::get_indices() [with M = beachmat::lin_matrix >; Rcpp::Vector<13>::iterator = int*; Rcpp::traits::storage_type<13>::type = int]':
cosine_norm.cpp:50:47: required from 'SEXPREC* cosine_norm_internal(SEXP, SEXP) [with M = beachmat::lin_matrix >; SEXP = SEXPREC*]'
cosine_norm.cpp:72:79: required from here
C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include/beachmat/utils/const_column.h:66:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -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/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c find_mutual_nns.cpp -o find_mutual_nns.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -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/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -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/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c smooth_gaussian_kernel.cpp -o smooth_gaussian_kernel.o
smooth_gaussian_kernel.cpp: In function 'SEXPREC* smooth_gaussian_kernel(SEXP, SEXP, SEXP, SEXP)':
smooth_gaussian_kernel.cpp:20:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (npairs!=_index.size()) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -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/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c unlog_exprs.cpp -o unlog_exprs.o
unlog_exprs.cpp: In function 'SEXPREC* unlog_exprs_scaled(SEXP, SEXP, SEXP, SEXP, SEXP)':
unlog_exprs.cpp:51:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (slen!=rescaling.size()) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -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/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::IntegerVector check_subset_vector(SEXP, size_t)':
utils.cpp:9:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (isNA(s) || s < 0 || s >= len) {
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o batchelor.dll tmp.def adjust_shift_variance.o cosine_norm.o find_mutual_nns.o init.o smooth_gaussian_kernel.o unlog_exprs.o utils.o -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/batchelor.buildbin-libdir/batchelor/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'batchelor' as batchelor_1.0.1.zip
* DONE (batchelor)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'batchelor' successfully unpacked and MD5 sums checked