Leonard Goldstein
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SGSeq |
| Branch: master |
| Last Commit: 4d31337 |
| Last Changed Date: 2018-12-18 20:26:44 -0400 (Tue, 18 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:21:47 -0400 (Tue, 09 Apr 2019).
| Package 1476/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SGSeq 1.17.2 Leonard Goldstein
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: SGSeq |
| Version: 1.17.2 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SGSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SGSeq_1.17.2.tar.gz |
| StartedAt: 2019-04-09 05:54:02 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 06:06:59 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 777.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SGSeq.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SGSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SGSeq_1.17.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SGSeq.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SGSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SGSeq' version '1.17.2'
* 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 'SGSeq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'GenomicRanges:::extraColumnSlotNames'
'GenomicRanges:::extraColumnSlotsAsDF'
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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
predictVariantEffects 29.41 0.17 29.58
analyzeFeatures 17.30 0.34 19.03
predictTxFeatures 8.47 0.11 8.58
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
predictVariantEffects 30.92 0.08 31.00
analyzeFeatures 16.69 0.44 17.12
predictTxFeatures 11.49 0.11 11.60
getSGVariantCounts 5.59 0.22 5.81
getSGFeatureCounts 5.19 0.09 5.28
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/SGSeq.Rcheck/00check.log'
for details.
SGSeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SGSeq_1.17.2.tar.gz && rm -rf SGSeq.buildbin-libdir && mkdir SGSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SGSeq.buildbin-libdir SGSeq_1.17.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SGSeq_1.17.2.zip && rm SGSeq_1.17.2.tar.gz SGSeq_1.17.2.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 1374k 100 1374k 0 0 18.2M 0 --:--:-- --:--:-- --:--:-- 19.7M
install for i386
* installing *source* package 'SGSeq' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SGSeq'
finding HTML links ... done
SGFeatureCounts html
SGFeatures html
SGSegments html
SGVariantCounts html
SGVariants html
TxFeatures html
analyzeFeatures html
analyzeVariants html
annotate html
annotateSGVariants html
assays html
convertToSGFeatures html
convertToTxFeatures html
exonCompatible html
exportFeatures html
filterFeatures html
findOverlapsRanges html
findSGVariants html
getBamInfo html
getSGFeatureCounts html
getSGFeatureCountsPerSample html
getSGVariantCounts html
gr html
importTranscripts html
junctionCompatible html
makeSGFeatureCounts html
makeVariantNames html
mergeTxFeatures html
plotCoverage html
plotFeatures html
plotSpliceGraph html
plotVariants html
predictCandidatesInternal html
predictCandidatesTerminal html
predictExonsInternal html
predictExonsTerminal html
predictJunctions html
predictSpliced html
predictTxFeatures html
predictTxFeaturesPerSample html
predictTxFeaturesPerStrand html
predictVariantEffects html
processTerminalExons html
removeExonsIsolated html
sgf_ann html
sgf_pred html
sgfc_ann html
sgfc_pred html
sgv_ann html
sgv_pred html
sgvc_ann html
sgvc_ann_from_bam html
sgvc_pred html
sgvc_pred_from_bam html
si html
slots html
splicesiteOverlap html
tx html
txf_ann html
txf_pred html
updateObject 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 'SGSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SGSeq' as SGSeq_1.17.2.zip
* DONE (SGSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SGSeq' successfully unpacked and MD5 sums checked
|
SGSeq.Rcheck/tests_i386/runTests.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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("SGSeq")
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, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply, rowsum
Predict features...
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Process features...
Obtain counts...
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: rtracklayer
Predicting effect of 2 variants on 3 coding transcripts...
Predicting effect of 3 variants on 3 coding transcripts...
RUNIT TEST PROTOCOL -- Tue Apr 09 06:04:04 2019
***********************************************
Number of test functions: 17
Number of errors: 0
Number of failures: 0
1 Test Suite :
SGSeq RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
131.09 2.12 133.92
|
SGSeq.Rcheck/tests_x64/runTests.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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("SGSeq")
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, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply, rowsum
Predict features...
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Process features...
Obtain counts...
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
Find segments...
Find variants...
Annotate variants...
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
N1 complete.
N2 complete.
N3 complete.
N4 complete.
T1 complete.
T2 complete.
T3 complete.
T4 complete.
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: rtracklayer
Predicting effect of 2 variants on 3 coding transcripts...
Predicting effect of 3 variants on 3 coding transcripts...
RUNIT TEST PROTOCOL -- Tue Apr 09 06:06:50 2019
***********************************************
Number of test functions: 17
Number of errors: 0
Number of failures: 0
1 Test Suite :
SGSeq RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
161.43 2.21 164.92
|
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SGSeq.Rcheck/examples_i386/SGSeq-Ex.timings
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SGSeq.Rcheck/examples_x64/SGSeq-Ex.timings
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