H. Pagès
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/SplicingGraphs |
| Branch: RELEASE_3_6 |
| Last Commit: 8e42e38 |
| Last Changed Date: 2017-10-30 12:40:02 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:22:48 -0400 (Thu, 12 Apr 2018).
| Package 1337/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SplicingGraphs 1.18.0 H. Pagès
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| Package: SplicingGraphs |
| Version: 1.18.0 |
| Command: rm -rf SplicingGraphs.buildbin-libdir SplicingGraphs.Rcheck && mkdir SplicingGraphs.buildbin-libdir SplicingGraphs.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SplicingGraphs.buildbin-libdir SplicingGraphs_1.18.0.tar.gz >SplicingGraphs.Rcheck\00install.out 2>&1 && cp SplicingGraphs.Rcheck\00install.out SplicingGraphs-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SplicingGraphs.buildbin-libdir --install="check:SplicingGraphs-install.out" --force-multiarch --no-vignettes --timings SplicingGraphs_1.18.0.tar.gz |
| StartedAt: 2018-04-12 03:22:26 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:32:24 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 597.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SplicingGraphs.Rcheck |
| Warnings: 3 |
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###
### Running command:
###
### rm -rf SplicingGraphs.buildbin-libdir SplicingGraphs.Rcheck && mkdir SplicingGraphs.buildbin-libdir SplicingGraphs.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SplicingGraphs.buildbin-libdir SplicingGraphs_1.18.0.tar.gz >SplicingGraphs.Rcheck\00install.out 2>&1 && cp SplicingGraphs.Rcheck\00install.out SplicingGraphs-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SplicingGraphs.buildbin-libdir --install="check:SplicingGraphs-install.out" --force-multiarch --no-vignettes --timings SplicingGraphs_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SplicingGraphs.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SplicingGraphs/DESCRIPTION' ... OK
* this is package 'SplicingGraphs' version '1.18.0'
* package encoding: UTF-8
* 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 'SplicingGraphs' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:69: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:71: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:97: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:106: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:123: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:124: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:126: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:130: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:131: missing file link 'exonsBy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:135: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:137: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:145: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:145: missing file link 'CharacterList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:151: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:159: missing file link 'exonsBy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:160: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:163: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:188: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:189: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:220: missing file link 'exonsBy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:222: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:225: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:228: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:228: missing file link 'CharacterList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:231: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:30: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:31: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:32: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:51: missing file link 'readGAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:69: missing file link 'readGAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:74: missing file link 'scanBamFlag'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:75: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:86: missing file link 'scanBamFlag'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:112: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:115: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:116: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:118: missing file link 'readGAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:122: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/countReads-methods.Rd:116: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:26: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:28: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:32: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:33: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:66: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:69: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:70: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:73: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/rsgedgesByGene-methods.Rd:81: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/sgedgesByGene-methods.Rd:21: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/sgedgesByGene-methods.Rd:27: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/sgedgesByGene-methods.Rd:63: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/toy_data.Rd:36: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/toy_data.Rd:39: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/toy_data.Rd:40: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/toy_data.Rd:44: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/txpath-methods.Rd:35: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/txpath-methods.Rd:69: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/txpath-methods.Rd:72: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/txpath-methods.Rd:73: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/txpath-methods.Rd:82: missing file link 'ScanBamParam'
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SplicingGraphs.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'GenomicFeatures' 'GenomicAlignments' 'Rgraphviz' 'igraph'
A package should be listed in only one of these fields.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'igraph' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
'S4Vectors:::matchIntegerPairs' 'S4Vectors:::orderIntegerPairs'
'S4Vectors:::selfmatchIntegerPairs'
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
'BiocGenerics:::testPackage' 'GenomicAlignments:::fillJunctionGaps'
'GenomicFeatures:::.collapse_df' 'IRanges:::newCompressedList0'
'IRanges:::regroupBySupergroup' 'S4Vectors:::setPrototypeFromObject'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'reportReads'
Undocumented S4 methods:
generic '[' and siglist 'SplicingGraphs,ANY,ANY,ANY'
generic 'reportReads' and siglist 'SplicingGraphs'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'countReads-methods':
'reportReads'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscripts-methods 26.55 0.27 26.90
toy_data 12.34 0.00 12.34
countReads-methods 5.65 0.00 5.66
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscripts-methods 27.78 0.10 28.42
toy_data 18.15 0.02 18.17
countReads-methods 5.80 0.00 5.80
rsgedgesByGene-methods 3.19 0.00 6.51
sgedgesByGene-methods 2.56 0.00 5.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R'
OK
** running tests for arch 'x64' ...
Running 'run_unitTests.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, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/SplicingGraphs.Rcheck/00check.log'
for details.
SplicingGraphs.Rcheck/00install.out
install for i386
* installing *source* package 'SplicingGraphs' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
** help
*** installing help indices
converting help for package 'SplicingGraphs'
finding HTML links ... done
SplicingGraphs-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:69: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:71: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:97: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:106: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:123: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:124: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:126: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:130: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:131: missing file link 'exonsBy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:135: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:137: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:145: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:145: missing file link 'CharacterList'
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Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:159: missing file link 'exonsBy'
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Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:189: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:220: missing file link 'exonsBy'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:222: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:225: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:228: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:228: missing file link 'CharacterList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/SplicingGraphs-class.Rd:231: missing file link 'DataFrame'
SplicingGraphs-package html
TSPCsg html
assignReads html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:30: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:31: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:32: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:51: missing file link 'readGAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:69: missing file link 'readGAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:74: missing file link 'scanBamFlag'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:75: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:86: missing file link 'scanBamFlag'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:112: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:115: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:116: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:118: missing file link 'readGAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/assignReads.Rd:122: missing file link 'ScanBamParam'
bubbles-methods html
countReads-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/countReads-methods.Rd:116: missing file link 'DataFrame'
plotTranscripts-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:26: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:28: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:32: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:33: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:66: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:69: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:70: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/plotTranscripts-methods.Rd:73: missing file link 'TxDb'
rsgedgesByGene-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/rsgedgesByGene-methods.Rd:81: missing file link 'GRangesList'
sgedges-methods html
sgedgesByGene-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/sgedgesByGene-methods.Rd:21: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/sgedgesByGene-methods.Rd:27: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/sgedgesByGene-methods.Rd:63: missing file link 'GRangesList'
sgraph-methods html
toy_data html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/toy_data.Rd:36: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/toy_data.Rd:39: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/toy_data.Rd:40: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/toy_data.Rd:44: missing file link 'TxDb'
txpath-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/txpath-methods.Rd:35: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/txpath-methods.Rd:69: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/txpath-methods.Rd:72: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/txpath-methods.Rd:73: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCWgM5q/R.INSTALL36f424b773c3/SplicingGraphs/man/txpath-methods.Rd:82: missing file link 'ScanBamParam'
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
In R CMD INSTALL
install for x64
* installing *source* package 'SplicingGraphs' ...
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
* MD5 sums
packaged installation of 'SplicingGraphs' as SplicingGraphs_1.18.0.zip
* DONE (SplicingGraphs)
In R CMD INSTALL
In R CMD INSTALL
|
SplicingGraphs.Rcheck/tests_i386/run_unitTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("SplicingGraphs") || stop("unable to load SplicingGraphs package")
Loading required package: SplicingGraphs
Loading required package: GenomicFeatures
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, cbind, colMeans, colSums, colnames, 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: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
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: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: Rgraphviz
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:Biostrings':
complement
Loading required package: grid
Attaching package: 'Rgraphviz'
The following objects are masked from 'package:IRanges':
from, to
The following objects are masked from 'package:S4Vectors':
from, to
[1] TRUE
Warning messages:
1: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
2: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
> SplicingGraphs:::.test()
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
RUNIT TEST PROTOCOL -- Thu Apr 12 03:32:03 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
SplicingGraphs RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
[samopen] SAM header is present: 1 sequences.
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
12.07 0.45 12.53
|
SplicingGraphs.Rcheck/tests_x64/run_unitTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("SplicingGraphs") || stop("unable to load SplicingGraphs package")
Loading required package: SplicingGraphs
Loading required package: GenomicFeatures
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, cbind, colMeans, colSums, colnames, 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: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
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: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
apply
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: Rgraphviz
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:Biostrings':
complement
Loading required package: grid
Attaching package: 'Rgraphviz'
The following objects are masked from 'package:IRanges':
from, to
The following objects are masked from 'package:S4Vectors':
from, to
[1] TRUE
Warning messages:
1: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
2: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
> SplicingGraphs:::.test()
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
RUNIT TEST PROTOCOL -- Thu Apr 12 03:32:19 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
SplicingGraphs RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
15.54 0.21 15.81
[samopen] SAM header is present: 1 sequences.
|
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SplicingGraphs.Rcheck/examples_i386/SplicingGraphs-Ex.timings
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SplicingGraphs.Rcheck/examples_x64/SplicingGraphs-Ex.timings
|