Michael Lawrence
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/biovizBase |
| Branch: RELEASE_3_8 |
| Last Commit: b6776d0 |
| Last Changed Date: 2018-12-11 14:49:53 -0400 (Tue, 11 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:21:51 -0400 (Sat, 13 Apr 2019).
| Package 162/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| biovizBase 1.30.1 Michael Lawrence
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: biovizBase |
| Version: 1.30.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biovizBase.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings biovizBase_1.30.1.tar.gz |
| StartedAt: 2019-04-13 00:50:57 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 00:57:56 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 419.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biovizBase.Rcheck |
| Warnings: 3 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biovizBase.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings biovizBase_1.30.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/biovizBase.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biovizBase/DESCRIPTION' ... OK
* this is package 'biovizBase' version '1.30.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'biovizBase' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpeM4VuY/R.INSTALL23206ac617f/biovizBase/man/crunch-method.Rd:31: file link 'AnnotationFilter-class' in package 'AnnotationFilter' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/biovizBase.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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' calls in package code:
'BSgenome' 'rtracklayer'
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
genSymbols: no visible binding for global variable 'start_location'
genSymbols: no visible binding for global variable 'end_location'
genSymbols: no visible binding for global variable 'Chromosome'
genSymbols: no visible binding for global variable 'symbol'
transformToLinkInCircle: no visible binding for global variable
'.circle.x'
transformToLinkInCircle: no visible binding for global variable
'.circle.y'
transformToLinkInCircle : <anonymous>: no visible binding for global
variable 'from.x'
transformToLinkInCircle : <anonymous>: no visible binding for global
variable 'from.y'
transformToLinkInCircle : <anonymous>: no visible binding for global
variable 'to.x'
transformToLinkInCircle : <anonymous>: no visible binding for global
variable 'to.y'
mold,ExpressionSet: no visible global function definition for 'exprs'
mold,ExpressionSet: no visible global function definition for 'pData'
mold,RleList: no visible binding for global variable 'xRleList'
mold,eSet: no visible global function definition for 'phenoData'
mold,eSet: no visible global function definition for 'melt'
mold,eSet: no visible global function definition for 'varLabels'
Undefined global functions or variables:
.circle.x .circle.y Chromosome end_location exprs from.x from.y melt
pData phenoData start_location symbol to.x to.y varLabels xRleList
* 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-3.8-bioc/R/library/biovizBase/libs/i386/biovizBase.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' ... WARNING
Found the following significant warnings:
Warning: 'GenenameFilter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
crunch-method 14.42 1.11 15.62
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
Warning: 'GenenameFilter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
crunch-method 13.84 0.48 14.33
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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: 3 WARNINGs, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/biovizBase.Rcheck/00check.log'
for details.
biovizBase.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/biovizBase_1.30.1.tar.gz && rm -rf biovizBase.buildbin-libdir && mkdir biovizBase.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biovizBase.buildbin-libdir biovizBase_1.30.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL biovizBase_1.30.1.zip && rm biovizBase_1.30.1.tar.gz biovizBase_1.30.1.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 2130k 100 2130k 0 0 17.7M 0 --:--:-- --:--:-- --:--:-- 18.4M
install for i386
* installing *source* package 'biovizBase' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_biovizBase.c -o R_init_biovizBase.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/R_ext/RS.h:34:0,
from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:37,
from bin_offsets.h:1,
from bin_offsets.c:3:
C:/Rtools/mingw_32/i686-w64-mingw32/include/string.h:76:15: note: expected 'const char *' but argument is of type 'Rbyte *'
int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/biovizBase.buildbin-libdir/biovizBase/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'biovizBase'
finding HTML links ... done
CRC html
GCcontent html
addStepping-method html
aes-utils html
biovizBase-package html
colorBlindSafePal html
containLetters html
crc1.GeRL html
crunch-method html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpeM4VuY/R.INSTALL23206ac617f/biovizBase/man/crunch-method.Rd:31: file link 'AnnotationFilter-class' in package 'AnnotationFilter' does not exist and so has been treated as a topic
darned_hg19_subset500 html
estimateCoverage-method html
flatGrl html
genesymbol html
getBioColor html
getFormalNames html
getGaps html
getIdeoGR html
getIdeogram html
getScale html
hg19Ideogram html
hg19IdeogramCyto html
ideo html
ideoCyto html
isIdeogram html
isMatchedWithModel html
isSimpleIdeogram html
labs html
maxGap-method html
mold-method html
finding level-2 HTML links ... done
pileupAsGRanges html
pileupGRangesAsVariantTable html
plotColorLegend html
scale html
showColor html
shrinkageFun-method html
splitByFacets-method html
strip_formula_dots html
subsetArgsByFormals html
transform html
transformGRangesForEvenSpace html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'biovizBase' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_biovizBase.c -o R_init_biovizBase.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
if (strncmp(b, "BAI\1", 4))
^
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/R_ext/RS.h:34:0,
from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:37,
from bin_offsets.h:1,
from bin_offsets.c:3:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/string.h:76:15: note: expected 'const char *' but argument is of type 'Rbyte *'
int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/biovizBase.buildbin-libdir/biovizBase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biovizBase' as biovizBase_1.30.1.zip
* DONE (biovizBase)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'biovizBase' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
biovizBase.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("biovizBase")
Loading required package: ensembldb
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
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
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: AnnotationFilter
Attaching package: 'ensembldb'
The following object is masked from 'package:stats':
filter
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
RUNIT TEST PROTOCOL -- Sat Apr 13 00:57:32 2019
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
biovizBase RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning message:
'GenenameFilter' is deprecated.
Use 'GeneNameFilter' instead.
See help("Deprecated")
>
> proc.time()
user system elapsed
13.92 1.34 15.95
|
biovizBase.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("biovizBase")
Loading required package: ensembldb
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: GenomicRanges
Loading required package: stats4
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
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: AnnotationFilter
Attaching package: 'ensembldb'
The following object is masked from 'package:stats':
filter
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
RUNIT TEST PROTOCOL -- Sat Apr 13 00:57:49 2019
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
biovizBase RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning message:
'GenenameFilter' is deprecated.
Use 'GeneNameFilter' instead.
See help("Deprecated")
>
> proc.time()
user system elapsed
16.29 0.64 16.92
|
|
biovizBase.Rcheck/examples_i386/biovizBase-Ex.timings
|
biovizBase.Rcheck/examples_x64/biovizBase-Ex.timings
|