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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:deepSNV.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings deepSNV_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/deepSNV.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.38.0’
* 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 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.
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 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 is not available
File ‘/home/biocbuild/bbs-3.13-bioc/R/library/deepSNV/libs/deepSNV.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘srand48’, possibly from ‘srand48’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

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. 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
RCC 5.848  0.124   5.999
* 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-3.13-bioc/meat/deepSNV.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL deepSNV
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘deepSNV’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-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*, int*, int*)’:
bam2R.cpp:97:13: warning: unused variable ‘iter’ [-Wunused-variable]
   97 |  hts_itr_t *iter = NULL;
      |             ^~~~
bam2R.cpp:100:6: warning: unused variable ‘c’ [-Wunused-variable]
  100 |  int c = 0;
      |      ^
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.13-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]
   27 |  int i, log=0;
      |         ^~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o deepSNV.so bam2R.o betabinom.o /home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-deepSNV/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (deepSNV)