| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:26 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the deepSNV package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 486/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| deepSNV 1.45.0 (landing page) Moritz Gerstung
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: deepSNV |
| Version: 1.45.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:deepSNV.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings deepSNV_1.45.0.tar.gz |
| StartedAt: 2022-12-28 23:04:36 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 23:09:41 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 305.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: deepSNV.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:deepSNV.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings deepSNV_1.45.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/deepSNV.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '1.45.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
installed size is 10.2Mb
sub-directories of 1Mb or more:
libs 8.3Mb
* 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 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 ... 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 ... 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 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-3.17-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 9.34 0.18 9.54
estimateDispersion-methods 5.08 0.25 5.33
* 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: 7 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/deepSNV.Rcheck/00check.log'
for details.
deepSNV.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL deepSNV
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'deepSNV' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam2R.cpp -o bam2R.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -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++11 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o F:/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-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 | 0 | 0 | |
| RCC | 9.34 | 0.18 | 9.54 | |
| RF | 0.00 | 0.02 | 0.02 | |
| bam2R | 0.02 | 0.00 | 0.02 | |
| betabinLRT | 0 | 0 | 0 | |
| consensusSequence-methods | 0.01 | 0.01 | 0.03 | |
| control-methods | 0 | 0 | 0 | |
| coordinates-methods | 0.00 | 0.02 | 0.01 | |
| counts | 0.02 | 0.00 | 0.02 | |
| deepSNV-class | 1.61 | 0.02 | 1.62 | |
| deepSNV-methods | 0.45 | 0.03 | 0.49 | |
| deepSNV-package | 0.45 | 0.01 | 0.47 | |
| estimateDirichlet-methods | 2.87 | 0.36 | 3.25 | |
| estimateDispersion-methods | 5.08 | 0.25 | 5.33 | |
| makePrior | 0 | 0 | 0 | |
| manhattanPlot | 1.39 | 0.00 | 1.39 | |
| normalize-methods | 3.41 | 0.06 | 3.47 | |
| p.combine | 0.62 | 0.05 | 0.67 | |
| p.val-methods | 0.00 | 0.02 | 0.02 | |
| phiX | 3.94 | 0.03 | 3.97 | |
| pi | 0.49 | 0.00 | 0.48 | |
| plot.deepSNV | 0.29 | 0.05 | 0.34 | |
| repeatMask-methods | 0.78 | 0.12 | 0.91 | |
| shearwater | 0.54 | 0.02 | 0.54 | |
| show-deepSNV-method | 0.29 | 0.01 | 0.35 | |
| summary-methods | 0.46 | 0.02 | 0.47 | |
| test-methods | 0.01 | 0.00 | 0.01 | |
| trueSNVs | 0.02 | 0.01 | 0.03 | |