##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TransView.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TransView_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TransView.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TransView/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TransView’ version ‘1.50.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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:
  parse_sam.c:161:88: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat]
  parse_sam.c:161:133: warning: format specifies type 'int' but the argument has type 'uint32_t *' (aka 'unsigned int *') [-Wformat]
  parse_sam.c:202:20: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat]
  parse_sam.c:203:47: warning: format specifies type 'int' but the argument has type 'long long' [-Wformat]
  parse_sam.c:315:18: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long long') [-Wformat]
  parse_sam.c:316:6: warning: format specifies type 'int' but the argument has type 'long long' [-Wformat]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/TransView.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/TransView/libs/TransView.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (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 sizes of PDF files under ‘inst/doc’ ... OK
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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