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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:deepSNV.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings deepSNV_1.48.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/deepSNV.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deepSNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deepSNV’ version ‘1.48.0’
* 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
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
* 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 loading without being on the library search path ... OK
* checking 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 ... 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.3.1/site-library/deepSNV/libs/deepSNV.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘sprintf’, possibly from ‘sprintf’ (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 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 ... ERROR
Running examples in ‘deepSNV-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RCC
> ### Title: Example RCC data
> ### Aliases: RCC
> 
> ### ** Examples
> 
> data("RCC", package="deepSNV")
> summary(RCC, adjust.method="bonferroni")[,1:6]
     chr      pos ref var         p.val      freq.var
6  chr10 89710231   C   T  1.812318e-06 -0.0522069105
1  chr17  7512879   G   A  4.923709e-03  0.0095680379
10 chr17  7513782   A   G  6.137099e-57  0.0523098637
15  chr3 10158255   A   -  7.414419e-27  0.0374605077
4   chr3 10158274   C   T 6.596999e-152 -0.1420210172
2   chr3 10158337   G   A  8.455105e-09 -0.1458150689
7   chr3 10163012   -   C 2.512916e-211  0.1242571351
16  chr3 10163206   T   -  0.000000e+00  0.2440387988
17  chr3 10163208   G   -  1.908223e-02  0.0007724394
11  chr3 10163428   T   G  1.026389e-79 -0.1111055718
8   chr3 10166219   G   C  6.538408e-74  0.1591560973
3   chr3 10166943   G   A 1.406981e-158 -0.1326056510
12  chr3 10167220   C   G  2.960126e-36  0.0046531880
13  chr3 10167672   A   G  0.000000e+00  0.1399833662
5   chr3 10167709   C   T 6.203881e-304 -0.1440968910
9   chr3 10167762   T   C  0.000000e+00 -0.1323353964
14  chr3 10168683   T   G 2.134656e-304 -0.1324914089
> plot(RCC)
> RCC.bb <- estimateDispersion(RCC, alternative="two.sided")
Note: The initial object used a binomial model. Will be changed to beta-binomial.
Estimated dispersion factor 136.926969822682 
> summary(RCC.bb, adjust.method="bonferroni")[,1:6]
   chr      pos ref var         p.val      freq.var
2 chr3 10158274   C   T  4.185434e-03 -0.1420210172
7 chr3 10163206   T   - 6.774267e-304  0.2440387988
8 chr3 10163208   G   -  2.693886e-02  0.0007724394
1 chr3 10166943   G   A  9.499952e-03 -0.1326056510
5 chr3 10167220   C   G  5.461018e-30  0.0046531880
3 chr3 10167709   C   T  3.466443e-02 -0.1440968910
4 chr3 10167762   T   C  8.715616e-03 -0.1323353964
6 chr3 10168683   T   G  4.237354e-02 -0.1324914089
> plot(RCC.bb)
* 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: 1 ERROR, 1 WARNING, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/deepSNV.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL deepSNV
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘deepSNV’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c bam2R.cpp -o bam2R.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-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++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o deepSNV.so bam2R.o betabinom.o /home/biocbuild/R/R-4.3.1/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-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)