Jun Woo
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ccfindR |
| Branch: master |
| Last Commit: f4e1273 |
| Last Changed Date: 2019-01-03 12:13:54 -0400 (Thu, 03 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:38:48 -0400 (Tue, 09 Apr 2019).
| Package 216/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ccfindR 1.3.0 Jun Woo
| 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: ccfindR |
| Version: 1.3.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ccfindR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ccfindR_1.3.0.tar.gz |
| StartedAt: 2019-04-09 01:34:30 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:39:30 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 300.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ccfindR.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ccfindR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ccfindR_1.3.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ccfindR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ccfindR/DESCRIPTION' ... OK
* this is package 'ccfindR' version '1.3.0'
* 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 'ccfindR' 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 ... NOTE
feature_map: no visible binding for global variable 'sd'
show,scNMFSet: no visible global function definition for 'head'
Undefined global functions or variables:
head sd
Consider adding
importFrom("stats", "sd")
importFrom("utils", "head")
to your NAMESPACE file.
* 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 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/ccfindR/libs/i386/ccfindR.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/ccfindR/libs/x64/ccfindR.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
factorize 8 0.05 8.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
factorize 8.11 0.01 8.12
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/ccfindR.Rcheck/00check.log'
for details.
ccfindR.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/ccfindR_1.3.0.tar.gz && rm -rf ccfindR.buildbin-libdir && mkdir ccfindR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ccfindR.buildbin-libdir ccfindR_1.3.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ccfindR_1.3.0.zip && rm ccfindR_1.3.0.tar.gz ccfindR_1.3.0.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 330k 100 330k 0 0 4989k 0 --:--:-- --:--:-- --:--:-- 5595k
install for i386
* installing *source* package 'ccfindR' ...
** 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/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.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/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c vbnmf_update.cpp -o vbnmf_update.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ccfindR.dll tmp.def RcppExports.o vbnmf_update.o -lgsl -lgslcblas -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/ccfindR.buildbin-libdir/00LOCK-ccfindR/00new/ccfindR/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ccfindR'
finding HTML links ... done
basis-scNMFSet-method html
basis-set-scNMFSet-method html
basis-set html
basis html
build_tree html
ccfindR html
cell_map html
cluster_id html
coeff-scNMFSet-method html
coeff-set-scNMFSet-method html
coeff-set html
coeff html
colData-scNMFSet-method html
colData-set-scNMFSet-ANY-method html
counts-scNMFSet-method html
counts-set-scNMFSet-method html
dbasis-scNMFSet-method html
dbasis-set-scNMFSet-method html
dbasis-set html
dbasis html
dcoeff-scNMFSet-method html
dcoeff-set-scNMFSet-method html
dcoeff-set html
dcoeff html
factorize html
feature_map html
filter_cells html
filter_genes html
gene_map html
measure-scNMFSet-method html
measure-set-scNMFSet-method html
measure-set html
measure html
meta_genes html
newick html
normalize_count html
optimal_rank html
plot_genes html
plot_tree html
finding level-2 HTML links ... done
ranks-scNMFSet-method html
ranks-set-scNMFSet-method html
ranks-set html
ranks html
read_10x html
remove_zeros html
rename_tips html
rowData-scNMFSet-method html
rowData-set-scNMFSet-method html
scNMFSet-class html
scNMFSet html
show-scNMFSet-method html
simulate_data html
simulate_whx html
subset-methods html
vb_factorize html
visualize_clusters html
write_10x 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 'ccfindR' ...
** 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/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.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/RcppEigen/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c vbnmf_update.cpp -o vbnmf_update.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ccfindR.dll tmp.def RcppExports.o vbnmf_update.o -lgsl -lgslcblas -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/ccfindR.buildbin-libdir/ccfindR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ccfindR' as ccfindR_1.3.0.zip
* DONE (ccfindR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ccfindR' successfully unpacked and MD5 sums checked
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ccfindR.Rcheck/examples_i386/ccfindR-Ex.timings
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ccfindR.Rcheck/examples_x64/ccfindR-Ex.timings
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