Sandro Morganella
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/VegaMC |
| git_branch: RELEASE_3_13 |
| git_last_commit: 37e7f4f |
| git_last_commit_date: 2021-05-19 11:51:55 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:27 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the VegaMC package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VegaMC.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2002/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VegaMC 3.30.0 (landing page) Sandro Morganella
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: VegaMC |
| Version: 3.30.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VegaMC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings VegaMC_3.30.0.tar.gz |
| StartedAt: 2021-10-15 07:10:39 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 07:13:44 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 185.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: VegaMC.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VegaMC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings VegaMC_3.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/VegaMC.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'VegaMC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VegaMC' version '3.30.0'
* 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 'VegaMC' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
example 4.9Mb
* 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 ... NOTE
Namespace in Imports field not imported from: 'methods'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getGenes: no visible global function definition for 'write.table'
qvalue: no visible global function definition for 'smooth.spline'
qvalue: no visible global function definition for 'predict'
vegaMC,character: no visible global function definition for
'read.table'
vegaMC,character: no visible global function definition for
'write.table'
Undefined global functions or variables:
predict read.table smooth.spline write.table
Consider adding
importFrom("stats", "predict", "smooth.spline")
importFrom("utils", "read.table", "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 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-3.13-bioc/R/library/VegaMC/libs/i386/VegaMC.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/VegaMC/libs/x64/VegaMC.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'rand', possibly from 'rand' (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
** 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/VegaMC.Rcheck/00check.log'
for details.
VegaMC.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/VegaMC_3.30.0.tar.gz && rm -rf VegaMC.buildbin-libdir && mkdir VegaMC.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VegaMC.buildbin-libdir VegaMC_3.30.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL VegaMC_3.30.0.zip && rm VegaMC_3.30.0.tar.gz VegaMC_3.30.0.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
50 1613k 50 816k 0 0 1663k 0 --:--:-- --:--:-- --:--:-- 1665k
100 1613k 100 1613k 0 0 2065k 0 --:--:-- --:--:-- --:--:-- 2065k
install for i386
* installing *source* package 'VegaMC' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c: In function 'read_params':
run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable]
char *elem, *brkt;
^~~~
run_vegaMC.c: In function 'load_data':
run_vegaMC.c:534:32: warning: 'chr' may be used uninitialized in this function [-Wmaybe-uninitialized]
temp_probe->chromosome = chr;
~~~~~~~~~~~~~~~~~~~~~~~^~~~~
run_vegaMC.c:535:30: warning: 'position' may be used uninitialized in this function [-Wmaybe-uninitialized]
temp_probe->position = position;
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
run_vegaMC.c:564:14: warning: 'first_probe' may be used uninitialized in this function [-Wmaybe-uninitialized]
prev_chr = temp_probe->chromosome;
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
run_vegaMC.c: In function 'call_VegaMC':
run_vegaMC.c:466:38: warning: 'first_seg' may be used uninitialized in this function [-Wmaybe-uninitialized]
seg_chromosomes[j] = (tmp->chromosome) + 1;
~~~~^~~~~~~~~~~~~
run_vegaMC.c:435:32: warning: 'prev_seg' may be used uninitialized in this function [-Wmaybe-uninitialized]
prev_seg->next = tmp;
~~~~~~~~~~~~~~~^~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sort_data.c -o sort_data.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vegaMC.c -o vegaMC.o
vegaMC.c: In function 'heap_delete':
vegaMC.c:235:10: warning: variable 'deleted' set but not used [-Wunused-but-set-variable]
node deleted;
^~~~~~~
vegaMC.c: In function 'init_trivial_segmentation':
vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable]
int i, j, index;
^~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o VegaMC.dll tmp.def run_vegaMC.o sort_data.o vegaMC.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/VegaMC.buildbin-libdir/00LOCK-VegaMC/00new/VegaMC/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'VegaMC'
finding HTML links ... done
VegaMC-package html
sortData html
vegaMC-methods html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/VegaMC.buildbin-libdir/00LOCK-VegaMC/00new/VegaMC/help/vegaMC.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 'VegaMC' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c: In function 'read_params':
run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable]
char *elem, *brkt;
^~~~
run_vegaMC.c: In function 'load_data':
run_vegaMC.c:534:32: warning: 'chr' may be used uninitialized in this function [-Wmaybe-uninitialized]
temp_probe->chromosome = chr;
~~~~~~~~~~~~~~~~~~~~~~~^~~~~
run_vegaMC.c:535:30: warning: 'position' may be used uninitialized in this function [-Wmaybe-uninitialized]
temp_probe->position = position;
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
run_vegaMC.c:564:14: warning: 'first_probe' may be used uninitialized in this function [-Wmaybe-uninitialized]
prev_chr = temp_probe->chromosome;
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
run_vegaMC.c: In function 'call_VegaMC':
run_vegaMC.c:466:38: warning: 'first_seg' may be used uninitialized in this function [-Wmaybe-uninitialized]
seg_chromosomes[j] = (tmp->chromosome) + 1;
~~~~^~~~~~~~~~~~~
run_vegaMC.c:435:32: warning: 'prev_seg' may be used uninitialized in this function [-Wmaybe-uninitialized]
prev_seg->next = tmp;
~~~~~~~~~~~~~~~^~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sort_data.c -o sort_data.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vegaMC.c -o vegaMC.o
vegaMC.c: In function 'heap_delete':
vegaMC.c:235:10: warning: variable 'deleted' set but not used [-Wunused-but-set-variable]
node deleted;
^~~~~~~
vegaMC.c: In function 'init_trivial_segmentation':
vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable]
int i, j, index;
^~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o VegaMC.dll tmp.def run_vegaMC.o sort_data.o vegaMC.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/VegaMC.buildbin-libdir/VegaMC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VegaMC' as VegaMC_3.30.0.zip
* DONE (VegaMC)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'VegaMC' successfully unpacked and MD5 sums checked
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VegaMC.Rcheck/examples_i386/VegaMC-Ex.timings
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VegaMC.Rcheck/examples_x64/VegaMC-Ex.timings
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