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CHECK report for deepSNV on malbec1

This page was generated on 2019-04-16 11:49:30 -0400 (Tue, 16 Apr 2019).

Package 383/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deepSNV 1.28.0
Moritz Gerstung
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/deepSNV
Branch: RELEASE_3_8
Last Commit: 9b6d747
Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: deepSNV
Version: 1.28.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:deepSNV.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings deepSNV_1.28.0.tar.gz
StartedAt: 2019-04-15 23:22:12 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:27:14 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 301.3 seconds
RetCode: 0
Status:  OK 
CheckDir: deepSNV.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:deepSNV.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings deepSNV_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/deepSNV.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deepSNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deepSNV’ version ‘1.28.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘parallel’ ‘Rhtslib’ ‘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 for sufficient/correct file permissions ... OK
* checking whether package ‘deepSNV’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Rhtslib’
A package should be listed in only one of these fields.
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’
.significantSNV: no visible global function definition for ‘p.adjust’
.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
  ‘scanVcfHeader’
.significantSNV: no visible global function definition for ‘metadata’
.significantSNV: no visible global function definition for ‘metadata<-’
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 ‘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 ‘scanVcfHeader’
bf2Vcf: no visible global function definition for ‘SimpleList’
bf2Vcf: no visible global function definition for ‘metadata’
bf2Vcf: no visible global function definition for ‘metadata<-’
bf2Vcf: no visible global function definition for ‘meta’
bf2Vcf: no visible global function definition for ‘meta<-’
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 ‘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 ‘scanVcfHeader’
qvals2Vcf: no visible global function definition for ‘SimpleList’
qvals2Vcf: no visible global function definition for ‘metadata’
qvals2Vcf: no visible global function definition for ‘metadata<-’
qvals2Vcf: no visible global function definition for ‘meta’
qvals2Vcf: no visible global function definition for ‘meta<-’
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 abline coefficients
  dirichlet info legend loess mclapply meta meta<- metadata metadata<-
  na.omit optimize p.adjust par pchisq pgamma pnorm scanVcfHeader
  seqnames
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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/deepSNV.Rcheck/00check.log’
for details.



Installation output

deepSNV.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL deepSNV
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘deepSNV’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for off_t... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function ‘int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)’:
bam2R.cpp:96:13: warning: unused variable ‘iter’ [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^
bam2R.cpp:99:6: warning: unused variable ‘c’ [-Wunused-variable]
  int c = 0;
      ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c betabinom.c -o betabinom.o
betabinom.c: In function ‘pbb’:
betabinom.c:27:9: warning: unused variable ‘log’ [-Wunused-variable]
  int i, log=0;
         ^
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o deepSNV.so bam2R.o betabinom.o -L/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/usrlib -Wl,-rpath,/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/deepSNV/libs
** 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
* DONE (deepSNV)

Tests output


Example timings

deepSNV.Rcheck/deepSNV-Ex.timings

nameusersystemelapsed
Extract-methods0.0080.0000.012
RCC4.6120.0724.687
RF0.0080.0000.006
bam2R0.0280.0000.057
betabinLRT000
consensusSequence-methods0.0240.0080.031
control-methods0.0080.0000.006
coordinates-methods0.0040.0000.006
counts0.0360.0000.039
deepSNV-class0.3400.0120.376
deepSNV-methods0.2960.0080.304
deepSNV-package0.1840.0160.200
estimateDirichlet-methods3.0960.0083.109
estimateDispersion-methods3.6320.0123.648
makePrior000
manhattanPlot0.1640.0040.167
normalize-methods1.8680.0001.871
p.combine0.1680.0000.170
p.val-methods0.0040.0000.005
phiX2.0440.0042.051
pi0.0800.0000.082
plot.deepSNV0.2000.0000.201
repeatMask-methods1.4840.0601.548
shearwater0.6520.0080.672
show-deepSNV-method0.1640.0040.170
summary-methods0.1680.0080.175
test-methods0.0040.0040.005
trueSNVs0.0200.0000.022