Davis McCarthy
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/scater |
| Branch: RELEASE_3_9 |
| Last Commit: 1518dc2 |
| Last Changed Date: 2019-05-23 18:48:27 -0400 (Thu, 23 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:35:00 -0400 (Wed, 16 Oct 2019).
| Package 1461/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scater 1.12.2 Davis McCarthy
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: scater |
| Version: 1.12.2 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scater.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings scater_1.12.2.tar.gz |
| StartedAt: 2019-10-16 06:54:41 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:06:44 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 723.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scater.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scater.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings scater_1.12.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/scater.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 'scater/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scater' version '1.12.2'
* 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 'scater' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/plotReducedDim.Rd:21: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:25: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:31: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:41: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:46: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:68: file link 'plotDiffusionMap' in package 'scater' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runMDS.Rd:62: file link 'plotMDS' in package 'scater' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runPCA.Rd:91: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runTSNE.Rd:74: file link 'Rtsne_neighbors' in package 'Rtsne' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runTSNE.Rd:95: file link 'plotTSNE' in package 'scater' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runUMAP.Rd:86: file link 'plotUMAP' in package 'scater' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/scater.Rcheck/00install.out' for details.
* 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 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/scater/libs/i386/scater.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/scater/libs/x64/scater.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
Examples with CPU or elapsed time > 5s
user system elapsed
plot_reddim 5.39 0.19 5.58
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot_reddim 5.22 0.1 5.31
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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
'C:/Users/biocbuild/bbs-3.9-bioc/meat/scater.Rcheck/00check.log'
for details.
scater.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/scater_1.12.2.tar.gz && rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scater.buildbin-libdir scater_1.12.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL scater_1.12.2.zip && rm scater_1.12.2.tar.gz scater_1.12.2.zip
###
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% 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 1145k 100 1145k 0 0 9.8M 0 --:--:-- --:--:-- --:--:-- 10.5M
install for i386
* installing *source* package 'scater' ...
** 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 calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of 'normalizer::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]':
calc_exprs.cpp:105:67: required from 'Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
calc_exprs.cpp:144:112: required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 0 || i >= nsets) {
^
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (current.size() != ncells) {
^
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (set_id.size()!=ptr->get_nrow()) {
^
calc_exprs.cpp: In instantiation of 'normalizer::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]':
calc_exprs.cpp:105:67: required from 'Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
calc_exprs.cpp:146:112: required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 0 || i >= nsets) {
^
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (current.size() != ncells) {
^
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (set_id.size()!=ptr->get_nrow()) {
^
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 combined_qc.cpp -o combined_qc.o
combined_qc.cpp: In function 'void check_topset(const IntegerVector&)':
combined_qc.cpp:15:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t t=1; t; IT = double*; typename V::iterator = int*; size_t = unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:274:109: required from 'SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:285:74: required from here
combined_qc.cpp:35:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (x; IT = double*; typename V::iterator = double*; size_t = unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:274:109: required from 'SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:287:74: required from here
combined_qc.cpp:35:35: 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 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 num_exprs.cpp -o num_exprs.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 sum_counts.cpp -o sum_counts.o
sum_counts.cpp: In function 'SEXPREC* sum_row_counts(SEXP, SEXP, SEXP, SEXP)':
sum_counts.cpp:72:18: warning: unused variable 'ncells' [-Wunused-variable]
const size_t ncells=end_index - start_index;
^
sum_counts.cpp: In instantiation of 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = unsigned int]':
sum_counts.cpp:150:83: required from here
sum_counts.cpp:96:18: warning: unused variable 'ncells' [-Wunused-variable]
const size_t ncells=mat->get_ncol();
^
sum_counts.cpp: In instantiation of 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = unsigned int]':
sum_counts.cpp:154:83: required from here
sum_counts.cpp:96:18: warning: unused variable 'ncells' [-Wunused-variable]
In file included from sum_counts.cpp:5:0:
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]':
sum_counts.cpp:120:49: required from 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = unsigned int]'
sum_counts.cpp:150:83: 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]':
sum_counts.cpp:120:49: required from 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = unsigned int]'
sum_counts.cpp:154:83: 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 utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o combined_qc.o init.o num_exprs.o sum_counts.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/scater.buildbin-libdir/00LOCK-scater/00new/scater/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'filter' in package 'scater'
** help
*** installing help indices
converting help for package 'scater'
finding HTML links ... done
SCESet html
accessors html
finding level-2 HTML links ... done
arrange html
bootstraps html
calculateAverage html
calculateCPM html
calculateFPKM html
calculateQCMetrics html
calculateTPM html
centreSizeFactors html
filter html
getBMFeatureAnnos html
getExplanatoryPCs html
getVarianceExplained html
isOutlier html
librarySizeFactors html
multiplot html
mutate html
nexprs html
normalize html
normalizeCounts html
plotColData html
plotExplanatoryPCs html
plotExplanatoryVariables html
plotExpression html
plotExprsFreqVsMean html
plotExprsVsTxLength html
plotHeatmap html
plotHighestExprs html
plotPlatePosition html
plotRLE html
plotReducedDim html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/plotReducedDim.Rd:21: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic
plotRowData html
plotScater html
plot_reddim html
readSparseCounts html
rename html
runDiffusionMap html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:25: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:31: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:41: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:46: file link 'DiffusionMap' in package 'destiny' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runDiffusionMap.Rd:68: file link 'plotDiffusionMap' in package 'scater' does not exist and so has been treated as a topic
runMDS html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runMDS.Rd:62: file link 'plotMDS' in package 'scater' does not exist and so has been treated as a topic
runPCA html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runPCA.Rd:91: file link 'plotPCA' in package 'scater' does not exist and so has been treated as a topic
runTSNE html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runTSNE.Rd:74: file link 'Rtsne_neighbors' in package 'Rtsne' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runTSNE.Rd:95: file link 'plotTSNE' in package 'scater' does not exist and so has been treated as a topic
runUMAP html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpO8jtKe/R.INSTALL243c4b581cae/scater/man/runUMAP.Rd:86: file link 'plotUMAP' in package 'scater' does not exist and so has been treated as a topic
sc_example_cell_info html
sc_example_counts html
scater-package html
scater-plot-args html
scater-vis-var html
sumCountsAcrossCells html
sumCountsAcrossFeatures html
toSingleCellExperiment html
uniquifyFeatureNames 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 'scater' ...
** 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 calc_exprs.cpp -o calc_exprs.o
calc_exprs.cpp: In instantiation of 'normalizer::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]':
calc_exprs.cpp:105:67: required from 'Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
calc_exprs.cpp:144:112: required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 0 || i >= nsets) {
^
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (current.size() != ncells) {
^
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (set_id.size()!=ptr->get_nrow()) {
^
calc_exprs.cpp: In instantiation of 'normalizer::normalizer(M*, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl]':
calc_exprs.cpp:105:67: required from 'Rcpp::RObject norm_exprs_internal(Rcpp::RObject, Rcpp::List, Rcpp::IntegerVector, Rcpp::RObject, Rcpp::RObject, Rcpp::RObject) [with M = beachmat::lin_matrix >; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::List = Rcpp::Vector<19>; Rcpp::IntegerVector = Rcpp::Vector<13>]'
calc_exprs.cpp:146:112: required from here
calc_exprs.cpp:24:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < 0 || i >= nsets) {
^
calc_exprs.cpp:39:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (current.size() != ncells) {
^
calc_exprs.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (set_id.size()!=ptr->get_nrow()) {
^
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 combined_qc.cpp -o combined_qc.o
combined_qc.cpp: In function 'void check_topset(const IntegerVector&)':
combined_qc.cpp:15:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t t=1; t; IT = double*; typename V::iterator = int*; size_t = long long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:274:109: required from 'SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:285:74: required from here
combined_qc.cpp:35:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (x; IT = double*; typename V::iterator = double*; size_t = long long unsigned int; Rcpp::IntegerVector = Rcpp::Vector<13>]':
combined_qc.cpp:274:109: required from 'SEXPREC* top_cumprop_internal(Rcpp::RObject, Rcpp::IntegerVector) [with M = beachmat::lin_matrix >; SEXP = SEXPREC*; Rcpp::RObject = Rcpp::RObject_Impl; Rcpp::IntegerVector = Rcpp::Vector<13>]'
combined_qc.cpp:287:74: required from here
combined_qc.cpp:35:35: 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 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 num_exprs.cpp -o num_exprs.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 sum_counts.cpp -o sum_counts.o
sum_counts.cpp: In function 'SEXPREC* sum_row_counts(SEXP, SEXP, SEXP, SEXP)':
sum_counts.cpp:72:18: warning: unused variable 'ncells' [-Wunused-variable]
const size_t ncells=end_index - start_index;
^
sum_counts.cpp: In instantiation of 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = long long unsigned int]':
sum_counts.cpp:150:83: required from here
sum_counts.cpp:96:18: warning: unused variable 'ncells' [-Wunused-variable]
const size_t ncells=mat->get_ncol();
^
sum_counts.cpp: In instantiation of 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = long long unsigned int]':
sum_counts.cpp:154:83: required from here
sum_counts.cpp:96:18: warning: unused variable 'ncells' [-Wunused-variable]
In file included from sum_counts.cpp:5:0:
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]':
sum_counts.cpp:120:49: required from 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = long long unsigned int]'
sum_counts.cpp:150:83: 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]':
sum_counts.cpp:120:49: required from 'Rcpp::RObject sum_col_counts_internal(Rcpp::RObject, const std::vector >&, size_t, size_t) [with M = beachmat::lin_matrix >; O = beachmat::lin_output >; Rcpp::RObject = Rcpp::RObject_Impl; size_t = long long unsigned int]'
sum_counts.cpp:154:83: 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 utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scater.dll tmp.def calc_exprs.o combined_qc.o init.o num_exprs.o sum_counts.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/scater.buildbin-libdir/scater/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scater' as scater_1.12.2.zip
* DONE (scater)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'scater' successfully unpacked and MD5 sums checked
|
scater.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(scater)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: ggplot2
Attaching package: 'scater'
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:stats':
filter
>
> test_check("scater")
== testthat results ===========================================================
[ OK: 1213 | SKIPPED: 2 | WARNINGS: 15 | FAILED: 0 ]
>
> proc.time()
user system elapsed
109.28 2.54 198.09
|
scater.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(scater)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: ggplot2
Attaching package: 'scater'
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:stats':
filter
>
> test_check("scater")
== testthat results ===========================================================
[ OK: 1213 | SKIPPED: 2 | WARNINGS: 15 | FAILED: 0 ]
>
> proc.time()
user system elapsed
108.57 2.03 182.71
|
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scater.Rcheck/examples_i386/scater-Ex.timings
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scater.Rcheck/examples_x64/scater-Ex.timings
|