Sandro Morganella
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Vega |
| Branch: RELEASE_3_9 |
| Last Commit: d08cfcd |
| Last Changed Date: 2019-05-02 11:53:20 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:24:34 -0400 (Wed, 16 Oct 2019).
| Package 1711/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Vega 1.32.0 Sandro Morganella
| 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 | WARNINGS | OK | |
| Package: Vega |
| Version: 1.32.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Vega.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Vega_1.32.0.tar.gz |
| StartedAt: 2019-10-16 07:49:14 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:49:46 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 32.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Vega.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Vega.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Vega_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Vega.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 'Vega/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Vega' version '1.32.0'
* 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 'Vega' 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
plotSegmentation: no visible global function definition for 'par'
plotSegmentation: no visible global function definition for 'plot'
plotSegmentation: no visible global function definition for 'lines'
vega: no visible global function definition for 'sd'
vega: no visible global function definition for 'write.table'
Undefined global functions or variables:
lines par plot sd write.table
Consider adding
importFrom("graphics", "lines", "par", "plot")
importFrom("stats", "sd")
importFrom("utils", "write.table")
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 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/Vega/libs/i386/Vega.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Vega/libs/x64/Vega.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/Vega.Rcheck/00check.log'
for details.
Vega.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/Vega_1.32.0.tar.gz && rm -rf Vega.buildbin-libdir && mkdir Vega.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Vega.buildbin-libdir Vega_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Vega_1.32.0.zip && rm Vega_1.32.0.tar.gz Vega_1.32.0.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 220k 100 220k 0 0 706k 0 --:--:-- --:--:-- --:--:-- 721k
install for i386
* installing *source* package 'Vega' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c vega.c -o vega.o
vega.c: In function 'heap_delete':
vega.c:201:8: warning: variable 'deleted' set but not used [-Wunused-but-set-variable]
node deleted;
^
vega.c: In function 'vega':
vega.c:355:13: warning: unused variable 'maxptr' [-Wunused-variable]
node max, *maxptr, tmp_node;
^
vega.c:348:68: warning: unused variable 'tmp_lambda2' [-Wunused-variable]
double lambda, lambda_gradient, stop_lambda_gradient, tmp_lambda, tmp_lambda2;
^
vega.c:347:6: warning: unused variable 'index' [-Wunused-variable]
int index;
^
vega.c: In function 'update_priority':
vega.c:560:64: warning: unused variable 'next_mean' [-Wunused-variable]
double lambda, first_term, second_term, prev_mean, curr_mean, next_mean;
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Vega.dll tmp.def vega.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/Vega.buildbin-libdir/00LOCK-Vega/00new/Vega/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Vega'
finding HTML links ... done
G519 html
Vega-package html
plotSegmentation html
vega 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 'Vega' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c vega.c -o vega.o
vega.c: In function 'heap_delete':
vega.c:201:8: warning: variable 'deleted' set but not used [-Wunused-but-set-variable]
node deleted;
^
vega.c: In function 'vega':
vega.c:355:13: warning: unused variable 'maxptr' [-Wunused-variable]
node max, *maxptr, tmp_node;
^
vega.c:348:68: warning: unused variable 'tmp_lambda2' [-Wunused-variable]
double lambda, lambda_gradient, stop_lambda_gradient, tmp_lambda, tmp_lambda2;
^
vega.c:347:6: warning: unused variable 'index' [-Wunused-variable]
int index;
^
vega.c: In function 'update_priority':
vega.c:560:64: warning: unused variable 'next_mean' [-Wunused-variable]
double lambda, first_term, second_term, prev_mean, curr_mean, next_mean;
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Vega.dll tmp.def vega.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/Vega.buildbin-libdir/Vega/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Vega' as Vega_1.32.0.zip
* DONE (Vega)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Vega' successfully unpacked and MD5 sums checked
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Vega.Rcheck/examples_i386/Vega-Ex.timings
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Vega.Rcheck/examples_x64/Vega-Ex.timings
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