Kent Riemondy
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/raer |
| git_branch: RELEASE_3_18 |
| git_last_commit: 852cee5 |
| git_last_commit_date: 2024-03-08 12:35:28 -0400 (Fri, 08 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:10 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1649/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| raer 1.0.2 (landing page) Kent Riemondy
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the raer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/raer.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: raer |
| Version: 1.0.2 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:raer.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings raer_1.0.2.tar.gz |
| StartedAt: 2024-03-28 04:08:48 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 04:18:51 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 602.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: raer.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:raer.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings raer_1.0.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/raer.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'raer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'raer' version '1.0.2'
* 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 'raer' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* checking installed package size ... NOTE
installed size is 10.1Mb
sub-directories of 1Mb or more:
libs 9.2Mb
* 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
* 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 ... OK
* 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 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/raer/libs/x64/raer.dll':
Found '_assert', possibly from 'assert' (C)
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (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 nor [v]sprintf. 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annot_snps 29.34 0.36 30.30
get_splice_sites 8.83 0.34 9.17
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.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 NOTEs
See
'F:/biocbuild/bbs-3.18-bioc/meat/raer.Rcheck/00check.log'
for details.
raer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL raer ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library' * installing *source* package 'raer' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.3.0' gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c plp.c -o plp.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c plp_data.c -o plp_data.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c plp_utils.c -o plp_utils.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c regfile.c -o regfile.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sc-plp.c -o sc-plp.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ext/bcftools/bcftools-ext.c -o ext/bcftools/bcftools-ext.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ext/htsbox/htsbox-ext.c -o ext/htsbox/htsbox-ext.o gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ext/samtools/samtools-ext.c -o ext/samtools/samtools-ext.o gcc -shared -s -static-libgcc -o raer.dll tmp.def init.o plp.o plp_data.o plp_utils.o regfile.o sc-plp.o utils.o ext/bcftools/bcftools-ext.o ext/htsbox/htsbox-ext.o ext/samtools/samtools-ext.o F:/biocbuild/bbs-3.18-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-raer/00new/raer/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (raer)
raer.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 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
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Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(raer)
>
> test_check("raer")
Using classic mode.
Attaching package: 'GenomicAlignments'
The following object is masked from 'package:data.table':
last
[raer internal] fail to parse region 'chr1' with F:/biocbuild/bbs-3.18-bioc/R/library/raer/extdata/SRR5564269_Aligned.sortedByCoord.out.md.bam
[raer internal] fail to parse region 'chrHello' with F:/biocbuild/bbs-3.18-bioc/R/library/raer/extdata/SRR5564269_Aligned.sortedByCoord.out.md.bam
Loading required package: SNPlocs.Hsapiens.dbSNP144.GRCh38
Loading required package: BSgenome
Loading required package: BiocIO
Attaching package: 'BiocIO'
The following object is masked from 'package:rtracklayer':
FileForFormat
Loading required package: BSgenome.Hsapiens.NCBI.GRCh38
i `filter_clustered_variants()`: removed 70 sites from 72 (2 remain)
i `filter_clustered_variants()`: removed 3 sites from 9 (6 remain)
i `filter_clustered_variants()`: removed 6 sites from 9 (3 remain)
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 261 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 261 ]
>
> proc.time()
user system elapsed
110.26 5.10 146.12
raer.Rcheck/raer-Ex.timings
| name | user | system | elapsed | |
| annot_from_gr | 1.27 | 0.09 | 1.45 | |
| annot_snps | 29.34 | 0.36 | 30.30 | |
| calc_AEI | 2.42 | 0.30 | 2.73 | |
| calc_confidence | 0.42 | 0.01 | 0.44 | |
| calc_edit_frequency | 0.61 | 0.07 | 0.67 | |
| calc_scAEI | 1.61 | 0.03 | 1.70 | |
| correct_strand | 0.69 | 0.01 | 0.71 | |
| filter_clustered_variants | 1.64 | 0.02 | 1.66 | |
| filter_multiallelic | 0.36 | 0.00 | 0.36 | |
| filter_splice_variants | 1.89 | 0.01 | 1.91 | |
| find_de_sites | 1.53 | 0.06 | 1.60 | |
| find_mispriming_sites | 0.58 | 0.00 | 0.58 | |
| find_scde_sites | 2.13 | 0.11 | 2.28 | |
| get_overlapping_snps | 3.18 | 0.08 | 3.27 | |
| get_splice_sites | 8.83 | 0.34 | 9.17 | |
| make_de_object | 0.67 | 0.05 | 0.72 | |
| mock_rse | 0.30 | 0.02 | 0.31 | |
| pileup_cells | 1.44 | 0.09 | 1.56 | |
| pileup_sites | 2.92 | 0.08 | 3.00 | |
| raer_example | 0.02 | 0.00 | 0.02 | |
| read_sparray | 1.45 | 1.11 | 4.09 | |