Julius Muller
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/TransView |
| Branch: RELEASE_3_10 |
| Last Commit: 8f39927 |
| Last Changed Date: 2019-10-29 13:08:35 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:21:04 -0400 (Wed, 15 Apr 2020).
| Package 1748/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TransView 1.30.0 Julius Muller
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: TransView |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TransView.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TransView_1.30.0.tar.gz |
| StartedAt: 2020-04-15 07:11:27 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:16:02 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 274.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TransView.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TransView.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TransView_1.30.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/TransView.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TransView/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TransView' version '1.30.0'
* 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 'TransView' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMP2iqM/R.INSTALL156c6f4331f/TransView/man/DensityContainer-class.Rd:137: file link 'slice1-methods' in package 'TransView' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMP2iqM/R.INSTALL156c6f4331f/TransView/man/DensityContainer-class.Rd:138: file link 'sliceN-methods' in package 'TransView' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMP2iqM/R.INSTALL156c6f4331f/TransView/man/DensityContainer-class.Rd:140: file link 'rmTV-methods' in package 'TransView' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMP2iqM/R.INSTALL156c6f4331f/TransView/man/TVResults-class.Rd:57: file link 'plotTVData-methods' in package 'TransView' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/TransView.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 6.5Mb
sub-directories of 1Mb or more:
libs 5.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for 'Rhtslib' is only usable in R >= 3.0.2
* 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
'library' or 'require' call to 'RUnit' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.gene2window : <anonymous> : <anonymous>: no visible global function
definition for 'median'
.gene2window: no visible binding for global variable 'approx'
.onAttach: no visible global function definition for
'packageDescription'
.test: no visible global function definition for 'defineTestSuite'
.test: no visible global function definition for 'runTestSuite'
.test: no visible global function definition for 'printTextProtocol'
annotatePeaks : <anonymous>: no visible global function definition for
'median'
gtf2gr: no visible global function definition for 'read.table'
gtf2gr: no visible global function definition for 'ave'
macs2gr: no visible global function definition for 'read.delim'
meltPeak: no visible global function definition for 'approx'
meltPeak: no visible global function definition for 'lowess'
plotTV: no visible global function definition for 'quantile'
plotTV: no visible global function definition for 'kmeans'
plotTV: no visible global function definition for 'as.dendrogram'
plotTV: no visible global function definition for 'hclust'
plotTV: no visible global function definition for 'as.dist'
plotTV: no visible global function definition for 'dist'
plotTV: no visible global function definition for 'order.dendrogram'
plotTV: no visible global function definition for 'par'
plotTV: no visible global function definition for 'layout'
plotTV: no visible global function definition for 'image'
plotTV: no visible global function definition for 'hist'
plotTV: no visible global function definition for 'title'
plotTV: no visible global function definition for 'mtext'
plotTV: no visible global function definition for 'lines'
plotTV: no visible global function definition for 'axis'
plotTV: no visible global function definition for 'rainbow'
plotTV: no visible global function definition for 'plot'
plotTV: no visible global function definition for 'text'
plotTV: no visible global function definition for 'rgb'
plotTV: no visible global function definition for 'plot.new'
setTV: no visible global function definition for 'object.size'
.setTV,DensityContainer-character-character-numeric-numeric-numeric-logical-character-character-logical:
no visible global function definition for 'object.size'
Undefined global functions or variables:
approx as.dendrogram as.dist ave axis defineTestSuite dist hclust
hist image kmeans layout lines lowess median mtext object.size
order.dendrogram packageDescription par plot plot.new
printTextProtocol quantile rainbow read.delim read.table rgb
runTestSuite text title
Consider adding
importFrom("grDevices", "rainbow", "rgb")
importFrom("graphics", "axis", "hist", "image", "layout", "lines",
"mtext", "par", "plot", "plot.new", "text", "title")
importFrom("stats", "approx", "as.dendrogram", "as.dist", "ave",
"dist", "hclust", "kmeans", "lowess", "median",
"order.dendrogram", "quantile")
importFrom("utils", "object.size", "packageDescription", "read.delim",
"read.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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* 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-3.10-bioc/R/library/TransView/libs/i386/TransView.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/TransView/libs/x64/TransView.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
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
Examples with CPU or elapsed time > 5s
user system elapsed
meltPeak 2.54 4.09 8.33
plotTV 2.00 4.40 7.31
slice1 1.62 4.58 6.78
plotTVData 1.75 4.38 6.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
meltPeak 3.31 4.95 8.43
slice1 2.28 5.24 7.69
plotTV 1.92 4.39 8.09
plotTVData 1.72 4.44 6.60
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'TransView_unit_tests.R'
OK
** running tests for arch 'x64' ...
Running 'TransView_unit_tests.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, 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/TransView.Rcheck/00check.log'
for details.
TransView.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TransView_1.30.0.tar.gz && rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TransView.buildbin-libdir TransView_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TransView_1.30.0.zip && rm TransView_1.30.0.tar.gz TransView_1.30.0.zip
###
##############################################################################
##############################################################################
% 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 980k 100 980k 0 0 2564k 0 --:--:-- --:--:-- --:--:-- 2593k
install for i386
* installing *source* package 'TransView' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_TransView.c -o R_init_TransView.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bin_density.c -o bin_density.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c construct_dc.c -o construct_dc.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/hts.h:35:0,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/sam.h:31,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/sam.h:28,
from parse_sam.h:4,
from construct_dc.c:23:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/hts_log.h:72:1: warning: 'Rprintf' is an unrecognized format function type [-Wformat=]
HTS_FORMAT(printf, 3, 4);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c parse_sam.c -o parse_sam.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sam.c -o sam.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c slice_dc.c -o slice_dc.o
slice_dc.c: In function 'slice_dc':
slice_dc.c:179:5: warning: 'slicep' may be used uninitialized in this function [-Wmaybe-uninitialized]
shrink(slicep,new_vecp,rebuildc,wsize,summarizep);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c visuals.c -o visuals.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o TransView.dll tmp.def R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o sam.o slice_dc.o visuals.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/TransView.buildbin-libdir/00LOCK-TransView/00new/TransView/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TransView'
finding HTML links ... done
DensityContainer-class html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMP2iqM/R.INSTALL156c6f4331f/TransView/man/DensityContainer-class.Rd:137: file link 'slice1-methods' in package 'TransView' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMP2iqM/R.INSTALL156c6f4331f/TransView/man/DensityContainer-class.Rd:138: file link 'sliceN-methods' in package 'TransView' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMP2iqM/R.INSTALL156c6f4331f/TransView/man/DensityContainer-class.Rd:140: file link 'rmTV-methods' in package 'TransView' does not exist and so has been treated as a topic
TVResults-class html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpMP2iqM/R.INSTALL156c6f4331f/TransView/man/TVResults-class.Rd:57: file link 'plotTVData-methods' in package 'TransView' does not exist and so has been treated as a topic
TransView-package html
annotatePeaks html
finding level-2 HTML links ... done
gtf2gr html
histogram-methods html
macs2gr html
meltPeak html
parseReads html
peak2tss html
plotTV html
plotTVData html
rmTV html
slice1 html
slice1T html
tvStats-methods 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 'TransView' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_TransView.c -o R_init_TransView.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bin_density.c -o bin_density.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c construct_dc.c -o construct_dc.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/hts.h:35:0,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/sam.h:31,
from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/sam.h:28,
from parse_sam.h:4,
from construct_dc.c:23:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/hts_log.h:72:1: warning: 'Rprintf' is an unrecognized format function type [-Wformat=]
HTS_FORMAT(printf, 3, 4);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c parse_sam.c -o parse_sam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sam.c -o sam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c slice_dc.c -o slice_dc.o
slice_dc.c: In function 'slice_dc':
slice_dc.c:179:5: warning: 'slicep' may be used uninitialized in this function [-Wmaybe-uninitialized]
shrink(slicep,new_vecp,rebuildc,wsize,summarizep);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c visuals.c -o visuals.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o TransView.dll tmp.def R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o sam.o slice_dc.o visuals.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/TransView.buildbin-libdir/TransView/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TransView' as TransView_1.30.0.zip
* DONE (TransView)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'TransView' successfully unpacked and MD5 sums checked
|
TransView.Rcheck/tests_i386/TransView_unit_tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
>
>
> require("TransView") || stop("unable to load TransView package")
Loading required package: TransView
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
Welcome to TransView version 1.30.0
Attaching package: 'TransView'
The following object is masked from 'package:GenomicRanges':
pos
The following object is masked from 'package:IRanges':
pos
The following object is masked from 'package:BiocGenerics':
pos
[1] TRUE
> TransView:::.test()
Version 2.09+ detected
21 peaks matching
172 rows matching
2862 rows matching
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit
Successful annotation within -5kBps to 2kBps: NA, 21 peaks without hit
Successful annotation within -5kBps to 2kBps: 10, 11 peaks without hit
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit
RUNIT TEST PROTOCOL -- Wed Apr 15 07:15:32 2020
***********************************************
Number of test functions: 9
Number of errors: 0
Number of failures: 0
1 Test Suite :
TransView RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
15.67 13.79 30.23
|
TransView.Rcheck/tests_x64/TransView_unit_tests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.
>
>
> require("TransView") || stop("unable to load TransView package")
Loading required package: TransView
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
Welcome to TransView version 1.30.0
Attaching package: 'TransView'
The following object is masked from 'package:GenomicRanges':
pos
The following object is masked from 'package:IRanges':
pos
The following object is masked from 'package:BiocGenerics':
pos
[1] TRUE
> TransView:::.test()
Version 2.09+ detected
21 peaks matching
172 rows matching
2862 rows matching
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit
Successful annotation within -5kBps to 2kBps: NA, 21 peaks without hit
Successful annotation within -5kBps to 2kBps: 10, 11 peaks without hit
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit
RUNIT TEST PROTOCOL -- Wed Apr 15 07:15:54 2020
***********************************************
Number of test functions: 9
Number of errors: 0
Number of failures: 0
1 Test Suite :
TransView RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
11.00 9.76 21.37
|
|
TransView.Rcheck/examples_i386/TransView-Ex.timings
|
TransView.Rcheck/examples_x64/TransView-Ex.timings
|