Package: fdrame

Version: 1.58.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fdrame.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fdrame_1.58.0.tar.gz

StartedAt: 2020-04-15 02:17:02 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:17:41 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 39.3 seconds

RetCode: 0

Status:  OK

CheckDir: fdrame.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fdrame.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fdrame_1.58.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/fdrame.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fdrame/DESCRIPTION’ ... OK
* this is package ‘fdrame’ version ‘1.58.0’
* 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 ‘fdrame’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
OnBrowseDesign: no visible binding for global variable ‘designFlag’
OnBrowseDesign: no visible binding for '<<-' assignment to ‘designFlag’
OnBrowseDesign: no visible binding for '<<-' assignment to
  ‘vector.list’
OnBrowseDesign: no visible binding for global variable ‘vector.list’
OnBrowseDesign: no visible binding for '<<-' assignment to
  ‘ttdesignlist’
OnBrowseDesign: no visible binding for '<<-' assignment to ‘tl’
OnBrowseDesign: no visible binding for global variable ‘ttdesignlist’
OnBrowseDesign: no visible binding for global variable ‘tl’
OnBrowseDesign: no visible binding for global variable ‘fdrtt’
OnBrowseInput: no visible binding for '<<-' assignment to
  ‘filename.input.tk’
OnBrowseInput: no visible binding for global variable
  ‘filename.input.tk’
OnBrowseInput: no visible binding for '<<-' assignment to
  ‘filename.input’
OnBrowseInput: no visible binding for global variable
  ‘entry.Filename.input’
OnBrowseInput: no visible binding for global variable ‘filename.input’
OnBrowseOutput: no visible binding for '<<-' assignment to
  ‘filename.output.tk’
OnBrowseOutput: no visible binding for global variable
  ‘filename.output.tk’
OnBrowseOutput: no visible binding for '<<-' assignment to
  ‘filename.output’
OnBrowseOutput: no visible binding for global variable
  ‘entry.Filename.output’
OnBrowseOutput: no visible binding for global variable
  ‘filename.output’
OnCancel: no visible binding for global variable ‘ttdesignlist’
OnCancel: no visible binding for global variable ‘fdrtt’
OnCancel: no visible binding for '<<-' assignment to ‘designFlag’
OnCbfa1: no visible binding for global variable ‘cbfa1Value’
OnCbfa1: no visible binding for '<<-' assignment to ‘cbfa5Value’
OnCbfa1: no visible binding for global variable ‘cbfa5’
OnCbfa2: no visible binding for global variable ‘cbfa2Value’
OnCbfa2: no visible binding for '<<-' assignment to ‘cbfa5Value’
OnCbfa2: no visible binding for global variable ‘cbfa5’
OnCbfa3: no visible binding for global variable ‘cbfa3Value’
OnCbfa3: no visible binding for '<<-' assignment to ‘cbfa5Value’
OnCbfa3: no visible binding for global variable ‘cbfa5’
OnCbfa4: no visible binding for global variable ‘cbfa4Value’
OnCbfa4: no visible binding for '<<-' assignment to ‘cbfa5Value’
OnCbfa4: no visible binding for global variable ‘cbfa5’
OnCompute: no visible binding for global variable ‘fdrtt’
OnCompute: no visible binding for global variable ‘rbnoValue’
OnCompute: no visible binding for global variable ‘rbfaValue’
OnCompute: no visible binding for global variable ‘cbpl1Value’
OnCompute: no visible binding for global variable ‘cbpl2Value’
OnCompute: no visible binding for global variable ‘cbpl3Value’
OnCompute: no visible binding for global variable ‘cbfa1Value’
OnCompute: no visible binding for global variable ‘cbfa2Value’
OnCompute: no visible binding for global variable ‘cbfa3Value’
OnCompute: no visible binding for global variable ‘cbfa4Value’
OnCompute: no visible binding for global variable ‘cbfa5Value’
OnCompute: no visible binding for global variable ‘filename.input’
OnCompute: no visible binding for global variable ‘filename.output’
OnCompute: no visible binding for global variable ‘design.tcl’
OnCompute: no visible binding for global variable ‘permsNum’
OnCompute: no visible binding for '<<-' assignment to ‘a’
OnOK: no visible binding for global variable ‘vector.list’
OnOK: no visible binding for global variable ‘tl’
OnOK: no visible binding for global variable ‘ttdesignlist’
OnOK: no visible binding for '<<-' assignment to ‘designVal’
OnOK: no visible binding for '<<-' assignment to ‘design.tcl’
OnOK: no visible binding for global variable ‘entry.Design’
OnOK: no visible binding for global variable ‘design.tcl’
OnOK: no visible binding for global variable ‘fdrtt’
OnOK: no visible binding for '<<-' assignment to ‘designFlag’
OnRbfa1: no visible binding for global variable ‘cbfa1’
OnRbfa1: no visible binding for global variable ‘cbfa2’
OnRbfa2: no visible binding for global variable ‘cbfa1’
OnRbfa2: no visible binding for global variable ‘cbfa2’
OnRbfa3: no visible binding for global variable ‘cbfa1’
OnRbfa3: no visible binding for global variable ‘cbfa2’
OnRbfa4: no visible binding for global variable ‘cbfa1’
OnRbfa4: no visible binding for global variable ‘cbfa2’
OnRbpm1: no visible binding for global variable ‘entry.Perms’
OnRbpm2: no visible binding for global variable ‘entry.Perms’
fdr.error: no visible binding for global variable ‘fdrtt’
fdr.gui: no visible binding for '<<-' assignment to ‘fdrtt’
fdr.gui: no visible binding for '<<-' assignment to ‘designFlag’
fdr.gui: no visible binding for '<<-' assignment to ‘frameOverall’
fdr.gui: no visible binding for global variable ‘fdrtt’
fdr.gui: no visible binding for '<<-' assignment to ‘frameCompute’
fdr.gui: no visible binding for global variable ‘frameOverall’
fdr.gui: no visible binding for '<<-' assignment to ‘frameInput’
fdr.gui: no visible binding for '<<-' assignment to ‘frameOutput’
fdr.gui: no visible binding for '<<-' assignment to ‘frameFileOutput’
fdr.gui: no visible binding for global variable ‘frameOutput’
fdr.gui: no visible binding for '<<-' assignment to ‘framePmethod’
fdr.gui: no visible binding for '<<-' assignment to ‘frameNorm’
fdr.gui: no visible binding for global variable ‘frameInput’
fdr.gui: no visible binding for '<<-' assignment to ‘frameAdj’
fdr.gui: no visible binding for '<<-' assignment to ‘framePerms’
fdr.gui: no visible binding for '<<-' assignment to ‘frameplot’
fdr.gui: no visible binding for '<<-' assignment to ‘filename.input’
fdr.gui: no visible binding for '<<-' assignment to ‘filename.output’
fdr.gui: no visible binding for '<<-' assignment to ‘design.tcl’
fdr.gui: no visible binding for '<<-' assignment to ‘permsNum’
fdr.gui: no visible binding for '<<-' assignment to
  ‘entry.Filename.input’
fdr.gui: no visible binding for global variable ‘filename.input’
fdr.gui: no visible binding for '<<-' assignment to
  ‘entry.Filename.output’
fdr.gui: no visible binding for global variable ‘filename.output’
fdr.gui: no visible binding for '<<-' assignment to ‘entry.Design’
fdr.gui: no visible binding for global variable ‘design.tcl’
fdr.gui: no visible binding for '<<-' assignment to ‘entry.Perms’
fdr.gui: no visible binding for global variable ‘frameAdj’
fdr.gui: no visible binding for global variable ‘permsNum’
fdr.gui: no visible binding for '<<-' assignment to ‘rbpm1’
fdr.gui: no visible binding for global variable ‘framePmethod’
fdr.gui: no visible binding for '<<-' assignment to ‘rbpm2’
fdr.gui: no visible binding for '<<-' assignment to ‘rbno1’
fdr.gui: no visible binding for '<<-' assignment to ‘rbno2’
fdr.gui: no visible binding for '<<-' assignment to ‘rbfa1’
fdr.gui: no visible binding for '<<-' assignment to ‘rbfa2’
fdr.gui: no visible binding for '<<-' assignment to ‘rbfa3’
fdr.gui: no visible binding for '<<-' assignment to ‘rbfa4’
fdr.gui: no visible binding for '<<-' assignment to ‘cbpl1’
fdr.gui: no visible binding for global variable ‘frameplot’
fdr.gui: no visible binding for '<<-' assignment to ‘cbpl2’
fdr.gui: no visible binding for '<<-' assignment to ‘cbpl3’
fdr.gui: no visible binding for '<<-' assignment to ‘cbfa1’
fdr.gui: no visible binding for '<<-' assignment to ‘cbfa2’
fdr.gui: no visible binding for '<<-' assignment to ‘cbfa3’
fdr.gui: no visible binding for '<<-' assignment to ‘cbfa4’
fdr.gui: no visible binding for '<<-' assignment to ‘cbfa5’
fdr.gui: no visible binding for '<<-' assignment to ‘rbpmValue’
fdr.gui: no visible binding for '<<-' assignment to ‘rbnoValue’
fdr.gui: no visible binding for '<<-' assignment to ‘rbfaValue’
fdr.gui: no visible binding for '<<-' assignment to ‘cbpl1Value’
fdr.gui: no visible binding for '<<-' assignment to ‘cbpl2Value’
fdr.gui: no visible binding for '<<-' assignment to ‘cbpl3Value’
fdr.gui: no visible binding for '<<-' assignment to ‘cbfa1Value’
fdr.gui: no visible binding for '<<-' assignment to ‘cbfa2Value’
fdr.gui: no visible binding for '<<-' assignment to ‘cbfa3Value’
fdr.gui: no visible binding for '<<-' assignment to ‘cbfa4Value’
fdr.gui: no visible binding for '<<-' assignment to ‘cbfa5Value’
fdr.gui: no visible binding for global variable ‘rbpm1’
fdr.gui: no visible binding for global variable ‘rbpmValue’
fdr.gui: no visible binding for global variable ‘rbpm2’
fdr.gui: no visible binding for global variable ‘rbno1’
fdr.gui: no visible binding for global variable ‘rbnoValue’
fdr.gui: no visible binding for global variable ‘rbno2’
fdr.gui: no visible binding for global variable ‘rbfa1’
fdr.gui: no visible binding for global variable ‘rbfaValue’
fdr.gui: no visible binding for global variable ‘rbfa2’
fdr.gui: no visible binding for global variable ‘rbfa3’
fdr.gui: no visible binding for global variable ‘rbfa4’
fdr.gui: no visible binding for global variable ‘cbpl1’
fdr.gui: no visible binding for global variable ‘cbpl1Value’
fdr.gui: no visible binding for global variable ‘cbpl2’
fdr.gui: no visible binding for global variable ‘cbpl2Value’
fdr.gui: no visible binding for global variable ‘cbpl3’
fdr.gui: no visible binding for global variable ‘cbpl3Value’
fdr.gui: no visible binding for global variable ‘cbfa1’
fdr.gui: no visible binding for global variable ‘cbfa1Value’
fdr.gui: no visible binding for global variable ‘cbfa2’
fdr.gui: no visible binding for global variable ‘cbfa2Value’
fdr.gui: no visible binding for global variable ‘cbfa3’
fdr.gui: no visible binding for global variable ‘cbfa3Value’
fdr.gui: no visible binding for global variable ‘cbfa4’
fdr.gui: no visible binding for global variable ‘cbfa4Value’
fdr.gui: no visible binding for global variable ‘cbfa5’
fdr.gui: no visible binding for global variable ‘cbfa5Value’
fdr.gui: no visible binding for global variable ‘entry.Perms’
fdr.gui: no visible binding for '<<-' assignment to ‘BrowseInput.but’
fdr.gui: no visible binding for '<<-' assignment to ‘BrowseDesign.but’
fdr.gui: no visible binding for '<<-' assignment to ‘BrowseOutput.but’
fdr.gui: no visible binding for '<<-' assignment to ‘Compute.but’
fdr.gui: no visible binding for global variable ‘frameCompute’
fdr.gui: no visible binding for '<<-' assignment to ‘Help.but’
fdr.gui: no visible binding for global variable ‘entry.Filename.input’
fdr.gui: no visible binding for global variable ‘BrowseInput.but’
fdr.gui: no visible binding for global variable ‘entry.Design’
fdr.gui: no visible binding for global variable ‘BrowseDesign.but’
fdr.gui: no visible binding for global variable ‘entry.Filename.output’
fdr.gui: no visible binding for global variable ‘BrowseOutput.but’
fdr.gui: no visible binding for global variable ‘Help.but’
fdr.gui: no visible binding for global variable ‘Compute.but’
Undefined global functions or variables:
  BrowseDesign.but BrowseInput.but BrowseOutput.but Compute.but
  Help.but cbfa1 cbfa1Value cbfa2 cbfa2Value cbfa3 cbfa3Value cbfa4
  cbfa4Value cbfa5 cbfa5Value cbpl1 cbpl1Value cbpl2 cbpl2Value cbpl3
  cbpl3Value design.tcl designFlag entry.Design entry.Filename.input
  entry.Filename.output entry.Perms fdrtt filename.input
  filename.input.tk filename.output filename.output.tk frameAdj
  frameCompute frameInput frameOutput frameOverall framePmethod
  frameplot permsNum rbfa1 rbfa2 rbfa3 rbfa4 rbfaValue rbno1 rbno2
  rbnoValue rbpm1 rbpm2 rbpmValue tl ttdesignlist vector.list
* 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/fdrame/libs/fdrame.so’:
  Found ‘_rand’, possibly from ‘rand’ (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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/fdrame.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL fdrame
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘fdrame’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fdr.c -o fdr.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o fdrame.so fdr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-fdrame/00new/fdrame/libs
** R
** data
** 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 (fdrame)

name	user	system	elapsed
design	0.019	0.004	0.022
exp.arr	0.007	0.001	0.008
fdrgui	0.064	0.010	0.079
fdrma	0.150	0.095	0.319