##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:TransView.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings TransView_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/TransView.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘TransView/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TransView’ version ‘1.49.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘TransView’ can be installed ... WARNING
Found the following significant warnings:
  /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/htslib/hts_log.h:76:1: warning: ‘Rprintf’ is an unrecognized format function type [-Wformat=]
  parse_sam.c:161:75: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  parse_sam.c:161:103: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘uint32_t *’ {aka ‘unsigned int *’} [-Wformat=]
  parse_sam.c:202:22: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  parse_sam.c:203:33: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  parse_sam.c:314:61: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  parse_sam.c:314:94: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/TransView.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘RUnit’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.gene2window : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
.gene2window: no visible binding for global variable ‘approx’
.onAttach: no visible global function definition for
  ‘packageDescription’
.test: no visible global function definition for ‘defineTestSuite’
.test: no visible global function definition for ‘runTestSuite’
.test: no visible global function definition for ‘printTextProtocol’
annotatePeaks : <anonymous>: no visible global function definition for
  ‘median’
gtf2gr: no visible global function definition for ‘read.table’
gtf2gr: no visible global function definition for ‘ave’
macs2gr: no visible global function definition for ‘read.delim’
meltPeak: no visible global function definition for ‘approx’
meltPeak: no visible global function definition for ‘lowess’
plotTV: no visible global function definition for ‘quantile’
plotTV: no visible global function definition for ‘kmeans’
plotTV: no visible global function definition for ‘as.dendrogram’
plotTV: no visible global function definition for ‘hclust’
plotTV: no visible global function definition for ‘as.dist’
plotTV: no visible global function definition for ‘dist’
plotTV: no visible global function definition for ‘order.dendrogram’
plotTV: no visible global function definition for ‘par’
plotTV: no visible global function definition for ‘layout’
plotTV: no visible global function definition for ‘image’
plotTV: no visible global function definition for ‘hist’
plotTV: no visible global function definition for ‘title’
plotTV: no visible global function definition for ‘mtext’
plotTV: no visible global function definition for ‘lines’
plotTV: no visible global function definition for ‘axis’
plotTV: no visible global function definition for ‘rainbow’
plotTV: no visible global function definition for ‘text’
plotTV: no visible global function definition for ‘rgb’
plotTV: no visible global function definition for ‘plot.new’
setTV: no visible global function definition for ‘object.size’
.setTV,DensityContainer-character-character-numeric-numeric-numeric-logical-character-character-logical:
  no visible global function definition for ‘object.size’
Undefined global functions or variables:
  approx as.dendrogram as.dist ave axis defineTestSuite dist hclust
  hist image kmeans layout lines lowess median mtext object.size
  order.dendrogram packageDescription par plot.new printTextProtocol
  quantile rainbow read.delim read.table rgb runTestSuite text title
Consider adding
  importFrom("grDevices", "rainbow", "rgb")
  importFrom("graphics", "axis", "hist", "image", "layout", "lines",
             "mtext", "par", "plot.new", "text", "title")
  importFrom("stats", "approx", "as.dendrogram", "as.dist", "ave",
             "dist", "hclust", "kmeans", "lowess", "median",
             "order.dendrogram", "quantile")
  importFrom("utils", "object.size", "packageDescription", "read.delim",
             "read.table")
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 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-3.20-bioc/R/site-library/TransView/libs/TransView.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘TransView_unit_tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/TransView.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL TransView
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘TransView’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_TransView.c -o R_init_TransView.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c bin_density.c -o bin_density.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c construct_dc.c -o construct_dc.o
In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/htslib/hts.h:36,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/htslib/sam.h:33,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/samtools-1.7-compat.h:5,
                 from parse_sam.h:4,
                 from construct_dc.c:23:
/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include/htslib/hts_log.h:76:1: warning: ‘Rprintf’ is an unrecognized format function type [-Wformat=]
   76 | HTS_FORMAT(HTS_PRINTF_FMT, 3, 4);
      | ^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c parse_sam.c -o parse_sam.o
parse_sam.c: In function ‘quality_check’:
parse_sam.c:161:75: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  161 |                         warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read));
      |                                                                          ~^                                 ~~~~~~~~~~~~~~~~~~~~~
      |                                                                           |                                                |
      |                                                                           int                                              hts_pos_t {aka long int}
      |                                                                          %ld
parse_sam.c:161:103: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘uint32_t *’ {aka ‘unsigned int *’} [-Wformat=]
  161 |                         warning("Read length neither found in core.isize=%d, core.l_qseq=%d or cigar=%d!\n",temp_read->core.isize,temp_read->core.l_qseq,bam1_cigar(temp_read));
      |                                                                                                      ~^
      |                                                                                                       |
      |                                                                                                       int
      |                                                                                                      %ls
parse_sam.c: In function ‘print_readinfo’:
parse_sam.c:202:22: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  202 |         printf("Pos %d\n",current_read->core.pos);
      |                     ~^    ~~~~~~~~~~~~~~~~~~~~~~
      |                      |                      |
      |                      int                    hts_pos_t {aka long int}
      |                     %ld
parse_sam.c:203:33: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  203 |         printf("Len %d -> END: %d\n",rm->read_length,rm->read_length+current_read->core.pos);
      |                                ~^                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                 |                                   |
      |                                 int                                 hts_pos_t {aka long int}
      |                                %ld
parse_sam.c: In function ‘seq_density’:
parse_sam.c:314:61: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  314 |                         warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n",
      |                                                            ~^
      |                                                             |
      |                                                             int
      |                                                            %ld
  315 |                                         BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND,
      |                                                     ~~~~~~~~~~~~~~~~~~~~~~
      |                                                                       |
      |                                                                       hts_pos_t {aka long int}
parse_sam.c:314:94: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=]
  314 |                         warning("BUFFER only %d\n But POS: %d cur_seq_len: %d EXTEND: %d -> %d \n GLOBAL %d\n",
      |                                                                                             ~^
      |                                                                                              |
      |                                                                                              int
      |                                                                                             %ld
  315 |                                         BUFFERLIMIT,current_read->core.pos,rm.read_length,user_args->EXTEND,
  316 |                                         current_read->core.pos+rm.read_length+user_args->EXTEND,abs_gen_end);
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                              |
      |                                                                              hts_pos_t {aka long int}
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c slice_dc.c -o slice_dc.o
slice_dc.c: In function ‘slice_dc’:
slice_dc.c:179:33: warning: ‘slicep’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  179 |                                 shrink(slicep,new_vecp,rebuildc,wsize,summarizep);
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c visuals.c -o visuals.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o TransView.so R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-TransView/00new/TransView/libs
** R
** 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 (TransView)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> 
> require("TransView") || stop("unable to load TransView package")
Loading required package: TransView
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Welcome to TransView version 1.49.0

Attaching package: 'TransView'

The following object is masked from 'package:GenomicRanges':

    pos

The following object is masked from 'package:IRanges':

    pos

The following object is masked from 'package:BiocGenerics':

    pos

[1] TRUE
> TransView:::.test()
Version 2.09+ detected
21 peaks matching
172 rows matching
2862 rows matching
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit
Successful annotation within -5kBps to 2kBps: NA, 21 peaks without hit
Successful annotation within -5kBps to 2kBps: 10, 11 peaks without hit
Successful annotation within -10kBps to 10kBps: 21, NA peaks without hit


RUNIT TEST PROTOCOL -- Thu Sep 12 04:07:47 2024 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
TransView RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  9.798   0.317  10.204