Moritz Gerstung
| Snapshot Date: 2024-11-21 13:40 -0500 (Thu, 21 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/deepSNV |
| git_branch: devel |
| git_last_commit: d480433 |
| git_last_commit_date: 2024-10-29 09:40:08 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-22 11:34 -0500 (Fri, 22 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" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4456 |
| 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 517/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| deepSNV 1.53.0 (landing page) Moritz Gerstung
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the deepSNV package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deepSNV.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: deepSNV |
| Version: 1.53.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:deepSNV.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings deepSNV_1.53.0.tar.gz |
| StartedAt: 2024-11-22 00:24:41 -0500 (Fri, 22 Nov 2024) |
| EndedAt: 2024-11-22 00:31:56 -0500 (Fri, 22 Nov 2024) |
| EllapsedTime: 435.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: deepSNV.Rcheck |
| Warnings: 0 |
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### Running command:
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### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:deepSNV.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings deepSNV_1.53.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/deepSNV.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'deepSNV/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'deepSNV' version '1.53.0'
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
'parallel', 'IRanges', 'GenomicRanges', 'SummarizedExperiment',
'Biostrings', 'VGAM', 'VariantAnnotation'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'deepSNV' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking installed package size ... INFO
installed size is 12.2Mb
sub-directories of 1Mb or more:
libs 10.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Versioned 'LinkingTo' value for 'Rhtslib' is only usable in R >= 3.0.2
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
'GenomicRanges' 'SummarizedExperiment' 'VariantAnnotation' 'parallel'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'estimateRho' 'logbb'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.deepSNVsingle: no visible global function definition for 'pchisq'
.estimateDispersion: no visible global function definition for
'optimize'
.makeVCFheader: no visible global function definition for 'splitAsList'
.makeVCFheader: no visible global function definition for 'DataFrame'
.significantSNV: no visible global function definition for 'p.adjust'
.significantSNV: no visible global function definition for
'scanVcfHeader'
.significantSNV: no visible global function definition for 'VCF'
.significantSNV: no visible global function definition for 'GRanges'
.significantSNV: no visible global function definition for 'IRanges'
.significantSNV: no visible global function definition for 'DataFrame'
.significantSNV: no visible global function definition for 'SimpleList'
.significantSNV: no visible global function definition for 'VCFHeader'
.significantSNV: no visible global function definition for 'reference'
.significantSNV: no visible global function definition for 'header'
bbb: no visible global function definition for 'na.omit'
betabinLRT: no visible global function definition for 'pchisq'
betabinLRT: no visible global function definition for 'p.adjust'
bf2Vcf: no visible global function definition for 'scanVcfHeader'
bf2Vcf: no visible global function definition for 'VCF'
bf2Vcf: no visible global function definition for 'GRanges'
bf2Vcf: no visible global function definition for 'IRanges'
bf2Vcf: no visible global function definition for 'DataFrame'
bf2Vcf: no visible global function definition for 'VCFHeader'
bf2Vcf: no visible global function definition for 'reference'
bf2Vcf: no visible global function definition for 'header'
bf2Vcf: no visible global function definition for 'SimpleList'
loadAllData: no visible global function definition for 'mclapply'
makePrior: no visible global function definition for 'info'
manhattanPlot: no visible global function definition for 'legend'
mcChunk: no visible global function definition for 'mclapply'
mutID: no visible global function definition for 'seqnames'
p.combine: no visible global function definition for 'pgamma'
plot.deepSNV: no visible global function definition for 'legend'
plot.deepSNV: no visible global function definition for 'par'
plot.deepSNV: no visible global function definition for 'abline'
qvals2Vcf: no visible global function definition for 'scanVcfHeader'
qvals2Vcf: no visible global function definition for 'VCF'
qvals2Vcf: no visible global function definition for 'GRanges'
qvals2Vcf: no visible global function definition for 'IRanges'
qvals2Vcf: no visible global function definition for 'DataFrame'
qvals2Vcf: no visible global function definition for 'VCFHeader'
qvals2Vcf: no visible global function definition for 'reference'
qvals2Vcf: no visible global function definition for 'header'
qvals2Vcf: no visible global function definition for 'SimpleList'
PCRTest,matrix-matrix: no visible global function definition for
'pnorm'
estimateDirichlet,matrix: no visible binding for global variable
'dirichlet'
estimateDirichlet,matrix: no visible global function definition for
'coefficients'
normalize,matrix-matrix : <anonymous>: no visible global function
definition for 'loess'
overDispersion,matrix-matrix: no visible global function definition for
'optimize'
overDispersion,matrix-matrix : <anonymous>: no visible global function
definition for 'na.omit'
Undefined global functions or variables:
DataFrame GRanges IRanges SimpleList VCF VCFHeader abline
coefficients dirichlet header info legend loess mclapply na.omit
optimize p.adjust par pchisq pgamma pnorm reference scanVcfHeader
seqnames splitAsList
Consider adding
importFrom("graphics", "abline", "legend", "par")
importFrom("stats", "coefficients", "loess", "na.omit", "optimize",
"p.adjust", "pchisq", "pgamma", "pnorm")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
bf2Vcf.Rd: VCF, GRanges
consensusSequence-methods.Rd: DNAString
deepSNV-methods.Rd: GRanges
qvals2Vcf.Rd: VCF, GRanges
repeatMask-methods.Rd: DNAString
summary-methods.Rd: VCF-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
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 'E:/biocbuild/bbs-3.21-bioc/R/library/deepSNV/libs/x64/deepSNV.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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RCC 13.62 0.24 13.86
estimateDispersion-methods 7.33 0.10 7.44
phiX 5.16 0.07 5.23
* 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: 5 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/deepSNV.Rcheck/00check.log'
for details.
deepSNV.Rcheck/00install.out
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### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL deepSNV
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'deepSNV' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam2R.cpp -o bam2R.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c betabinom.c -o betabinom.o
betabinom.c: In function 'pbb':
betabinom.c:27:16: warning: unused variable 'log' [-Wunused-variable]
27 | int i, log=0;
| ^~~
g++ -std=gnu++17 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o E:/biocbuild/bbs-3.21-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-deepSNV/00new/deepSNV/libs/x64
** R
** data
** 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 (deepSNV)
deepSNV.Rcheck/deepSNV-Ex.timings
| name | user | system | elapsed | |
| Extract-methods | 0.02 | 0.00 | 0.01 | |
| RCC | 13.62 | 0.24 | 13.86 | |
| RF | 0.01 | 0.00 | 0.01 | |
| bam2R | 0.02 | 0.01 | 0.03 | |
| betabinLRT | 0 | 0 | 0 | |
| consensusSequence-methods | 0.03 | 0.00 | 0.03 | |
| control-methods | 0.00 | 0.02 | 0.02 | |
| coordinates-methods | 0.01 | 0.01 | 0.03 | |
| counts | 0.02 | 0.02 | 0.03 | |
| deepSNV-class | 1.95 | 0.04 | 2.02 | |
| deepSNV-methods | 0.77 | 0.05 | 0.81 | |
| deepSNV-package | 0.67 | 0.02 | 0.69 | |
| estimateDirichlet-methods | 2.86 | 0.12 | 2.98 | |
| estimateDispersion-methods | 7.33 | 0.10 | 7.44 | |
| makePrior | 0 | 0 | 0 | |
| manhattanPlot | 1.42 | 0.03 | 1.45 | |
| normalize-methods | 4.28 | 0.06 | 4.35 | |
| p.combine | 0.78 | 0.03 | 0.81 | |
| p.val-methods | 0.00 | 0.02 | 0.02 | |
| phiX | 5.16 | 0.07 | 5.23 | |
| pi | 0.55 | 0.00 | 0.55 | |
| plot.deepSNV | 0.4 | 0.0 | 0.4 | |
| repeatMask-methods | 1.00 | 0.13 | 1.13 | |
| shearwater | 0.81 | 0.08 | 0.89 | |
| show-deepSNV-method | 0.43 | 0.03 | 0.45 | |
| summary-methods | 0.71 | 0.00 | 0.72 | |
| test-methods | 0.00 | 0.01 | 0.02 | |
| trueSNVs | 0.02 | 0.04 | 0.04 | |