Leonard Goldstein
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/SGSeq |
| git_branch: devel |
| git_last_commit: 193e8a3 |
| git_last_commit_date: 2024-10-29 09:56:07 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:17 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1926/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SGSeq 1.41.0 (landing page) Leonard Goldstein
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the SGSeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SGSeq.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SGSeq |
| Version: 1.41.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SGSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SGSeq_1.41.0.tar.gz |
| StartedAt: 2024-11-28 02:19:00 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 02:29:42 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 642.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SGSeq.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SGSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SGSeq_1.41.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SGSeq.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SGSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SGSeq’ version ‘1.41.0’
* 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 for sufficient/correct file permissions ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 ... NOTE
checkRd: (-1) SGVariants.Rd:24-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:32-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SGVariants.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getBamInfo.Rd:36: Lost braces; missing escapes or markup?
36 | Note that library size is only obtained if \code{yieldSize} is {NULL}.
| ^
checkRd: (-1) getSGFeatureCounts.Rd:28: Lost braces
28 | code{SGFeatureCounts} object, or integer matrix of counts
| ^
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
predictVariantEffects 32.366 0.297 37.337
analyzeFeatures 16.034 0.240 16.363
predictTxFeatures 8.357 0.080 8.464
getSGVariantCounts 5.340 0.065 5.433
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/SGSeq.Rcheck/00check.log’
for details.
SGSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SGSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘SGSeq’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (SGSeq)
SGSeq.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
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, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
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...
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
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.
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
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: BiocIO
Loading required package: rtracklayer
Attaching package: 'rtracklayer'
The following object is masked from 'package:BiocIO':
FileForFormat
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
Predicting effect of 2 variants on 3 coding transcripts...
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
Predicting effect of 3 variants on 3 coding transcripts...
RUNIT TEST PROTOCOL -- Thu Nov 28 02:29:34 2024
***********************************************
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
Warning message:
In (function (seqlevels, genome, new_style) :
cannot switch some hg19's seqlevels from UCSC to NCBI style
>
> proc.time()
user system elapsed
134.071 1.495 136.856
SGSeq.Rcheck/SGSeq-Ex.timings
| name | user | system | elapsed | |
| SGFeatureCounts | 0.756 | 0.007 | 0.765 | |
| SGFeatures | 0.037 | 0.000 | 0.037 | |
| SGVariantCounts | 0.152 | 0.003 | 0.154 | |
| SGVariants | 0.108 | 0.013 | 0.122 | |
| TxFeatures | 0.040 | 0.004 | 0.044 | |
| analyzeFeatures | 16.034 | 0.240 | 16.363 | |
| analyzeVariants | 1.407 | 0.015 | 1.428 | |
| annotate | 1.503 | 0.009 | 1.518 | |
| assays | 0.019 | 0.000 | 0.020 | |
| convertToSGFeatures | 1.006 | 0.005 | 1.016 | |
| convertToTxFeatures | 0.386 | 0.002 | 0.390 | |
| exportFeatures | 0 | 0 | 0 | |
| findSGVariants | 1.103 | 0.007 | 1.113 | |
| getBamInfo | 1.580 | 0.114 | 1.701 | |
| getSGFeatureCounts | 4.444 | 0.070 | 4.535 | |
| getSGVariantCounts | 5.340 | 0.065 | 5.433 | |
| importTranscripts | 0 | 0 | 0 | |
| makeSGFeatureCounts | 0.043 | 0.001 | 0.044 | |
| makeVariantNames | 0.015 | 0.000 | 0.015 | |
| mergeTxFeatures | 0.176 | 0.006 | 0.182 | |
| plotCoverage | 0.000 | 0.001 | 0.000 | |
| plotFeatures | 0 | 0 | 0 | |
| plotSpliceGraph | 0.000 | 0.000 | 0.001 | |
| plotVariants | 0 | 0 | 0 | |
| predictTxFeatures | 8.357 | 0.080 | 8.464 | |
| predictVariantEffects | 32.366 | 0.297 | 37.337 | |
| processTerminalExons | 0.2 | 0.0 | 0.2 | |
| slots | 0.001 | 0.001 | 0.001 | |