cydar 1.0.0
Aaron Lun
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/cydar | | Branch: RELEASE_3_5 | | Last Commit: a49b2cc | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings cydar_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/cydar.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cydar/DESCRIPTION’ ... OK
* this is package ‘cydar’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cydar’ 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
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘S4Vectors:::selectSome’
‘SummarizedExperiment:::.SummarizedExperiment.charbound’
See the note in ?`:::` about the use of this operator.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
diffIntDistr 11.820 0.180 12.013
normalizeBatch 6.628 0.008 6.645
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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 NOTE
See
‘/home/biocbuild/bbs-3.5-bioc/meat/cydar.Rcheck/00check.log’
for details.
* installing *source* package ‘cydar’ ...
** libs
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c compute_density.cpp -o compute_density.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c compute_hyperstats.cpp -o compute_hyperstats.o
compute_hyperstats.cpp: In function ‘SEXPREC* compute_hyperstats(SEXP, SEXP, SEXP, SEXP, SEXP)’:
compute_hyperstats.cpp:26:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (!isInteger(sample_id) || LENGTH(sample_id)!=ncells) {
^
compute_hyperstats.cpp:71:30: warning: variable ‘midweight’ set but not used [-Wunused-but-set-variable]
double total_weight, midweight, cumweight;
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c compute_median_int.cpp -o compute_median_int.o
compute_median_int.cpp: In function ‘SEXPREC* compute_median_int(SEXP, SEXP, SEXP, SEXP, SEXP)’:
compute_median_int.cpp:26:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (!isInteger(sample_id) || LENGTH(sample_id)!=ncells) {
^
compute_median_int.cpp:46:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=1; s<nsamples; ++s) {
^
compute_median_int.cpp:72:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (current < 0 || current >= ncells) {
^
compute_median_int.cpp:86:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (s=0; s<nsamples; ++s) {
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c count_cells.cpp -o count_cells.o
In file included from count_cells.cpp:2:0:
packer.h: In instantiation of ‘void pack_index_vector(std::deque<int>&, Iter, Iter) [with Iter = std::_Deque_iterator<long unsigned int, long unsigned int&, long unsigned int*>]’:
count_cells.cpp:46:77: required from here
packer.h:28:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ((*previous)+1!=sorted_ids.back()) {
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c drop_redundant.cpp -o drop_redundant.o
drop_redundant.cpp: In function ‘SEXPREC* drop_redundant(SEXP, SEXP, SEXP, SEXP, SEXP)’:
drop_redundant.cpp:17:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (LENGTH(actual_order)!=nhyper) {
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c get_nndist.cpp -o get_nndist.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c matrix_info.cpp -o matrix_info.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c objects.cpp -o objects.o
objects.cpp: In constructor ‘naive_holder::naive_holder(SEXP, SEXP)’:
objects.cpp:30:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int u=0; u<exprs.nrow; ++u) {
^
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pack_indices.cpp -o pack_indices.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c recount.cpp -o recount.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o cydar.so compute_density.o compute_hyperstats.o compute_median_int.o count_cells.o drop_redundant.o get_nndist.o init.o matrix_info.o objects.o pack_indices.o recount.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/cydar.Rcheck/cydar/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cydar)