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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:girafe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings girafe_1.58.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/girafe.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 ‘girafe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘girafe’ version ‘1.58.0’
* 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'
 NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'Rsamtools', 'intervals', 'ShortRead',
  'genomeIntervals', 'grid'
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 ‘girafe’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘genomeIntervals’
A package should be listed in only one of these fields.
* 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 ... NOTE
No methods found in package ‘IRanges’ for requests: ‘score’, ‘score<-’, ‘sort’ when loading ‘girafe’

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘MASS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘Rsamtools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘genomeIntervals:::intervalsForOverlap’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
agiFromBam: no visible binding for global variable ‘mclapply’
agiFromBam: no visible global function definition for ‘scanBamHeader’
agiFromBam: no visible global function definition for ‘ScanBamParam’
agiFromBam : <anonymous>: no visible global function definition for
  ‘scanBamFlag’
agiFromBam : <anonymous>: no visible global function definition for
  ‘scanBam’
countReadsAnnotated: no visible binding for global variable ‘mclapply’
countReadsAnnotated: no visible binding for global variable ‘fraction1’
fracOverlap: no visible binding for global variable ‘fraction1’
fracOverlap: no visible binding for global variable ‘fraction2’
getFeatureCounts: no visible binding for global variable ‘fraction1’
getFeatureCounts: no visible binding for global variable ‘Index1’
intPhred: no visible binding for global variable ‘mclapply’
oldAGIoverlap: no visible binding for global variable ‘mclapply’
plotReads: no visible binding for global variable ‘x.start’
plotReads: no visible binding for global variable ‘x.end’
plotReads: no visible binding for global variable ‘y’
reduceOne: no visible binding for global variable ‘fraction1’
reduceOne: no visible binding for global variable ‘fraction2’
windowCountAndGC: no visible binding for global variable ‘n.reads’
windowCountAndGC: no visible global function definition for ‘unmasked’
clusters,AlignedGenomeIntervals: no visible binding for global variable
  ‘mclapply’
clusters,Genome_intervals: no visible binding for global variable
  ‘mclapply’
coverage,AlignedGenomeIntervals: no visible binding for global variable
  ‘mclapply’
coverage,AlignedGenomeIntervals : <anonymous>: no visible binding for
  global variable ‘on.minus’
interval_included,AlignedGenomeIntervals-AlignedGenomeIntervals: no
  visible binding for global variable ‘mclapply’
reduce,AlignedGenomeIntervals: no visible binding for global variable
  ‘mclapply’
reduce,Genome_intervals: no visible binding for global variable
  ‘mclapply’
reduce,Genome_intervals: no visible binding for global variable
  ‘fraction1’
reduce,Genome_intervals: no visible binding for global variable
  ‘fraction2’
Undefined global functions or variables:
  Index1 ScanBamParam fraction1 fraction2 mclapply n.reads on.minus
  scanBam scanBamFlag scanBamHeader unmasked x.end x.start y
* 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 for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
negbinomsig 5.944  0.127   6.085
perWindow   5.863  0.095   5.967
* 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: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/girafe.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL girafe
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘girafe’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c coverage.cpp -o coverage.o
coverage.cpp:2:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c girafe_init.c -o girafe_init.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o girafe.so coverage.o girafe_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-girafe/00new/girafe/libs
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘IRanges’ for requests: ‘score’, ‘score<-’, ‘sort’ when loading ‘girafe’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘girafe’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘IRanges’ for requests: ‘score’, ‘score<-’, ‘sort’ when loading ‘girafe’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘IRanges’ for requests: ‘score’, ‘score<-’, ‘sort’ when loading ‘girafe’
** testing if installed package keeps a record of temporary installation path
* DONE (girafe)