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CHECK report for metahdep on merida1

This page was generated on 2019-04-16 11:55:00 -0400 (Tue, 16 Apr 2019).

Package 923/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metahdep 1.40.0
John R. Stevens
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/metahdep
Branch: RELEASE_3_8
Last Commit: 38f418c
Last Changed Date: 2018-10-30 11:41:45 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: metahdep
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metahdep.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metahdep_1.40.0.tar.gz
StartedAt: 2019-04-16 01:08:17 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:08:47 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 29.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: metahdep.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metahdep.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metahdep_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/metahdep.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metahdep/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metahdep’ version ‘1.40.0’
* 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 ‘metahdep’ can be installed ... WARNING
Found the following significant warnings:
  metahdep.c:471:79: warning: incompatible pointer to integer conversion passing 'const char *' to parameter of type 'char' [-Wint-conversion]
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/metahdep.Rcheck/00install.out’ for details.
* 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 ... NOTE
'library' or 'require' call to ‘affyPLM’ 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: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
LinMod.HBLM.fast.dep: no visible global function definition for ‘pnorm’
LinMod.MetAn.dep.FEMA: no visible global function definition for
  ‘pchisq’
LinMod.MetAn.dep.FEMA: no visible global function definition for ‘pt’
LinMod.MetAn.dep.REMA: no visible global function definition for
  ‘pchisq’
LinMod.MetAn.dep.REMA: no visible global function definition for ‘pt’
LinMod.REMA.delta.split: no visible global function definition for ‘pt’
LinMod.REMA.delta.split: no visible global function definition for
  ‘pchisq’
getPLM.es: no visible global function definition for ‘fitPLM’
getPLM.es: no visible global function definition for ‘coefs’
getPLM.es: no visible global function definition for ‘varcov’
getPLM.es: no visible global function definition for ‘new’
getPLM.es: no visible global function definition for ‘annotation’
metahdep: no visible global function definition for ‘flush.console’
metahdep.FEMA: no visible global function definition for ‘pchisq’
metahdep.FEMA: no visible global function definition for ‘pnorm’
metahdep.HBLM: no visible global function definition for ‘new’
metahdep.REMA: no visible global function definition for ‘new’
metahdep.format: no visible global function definition for ‘sd’
metahdep.format: no visible global function definition for
  ‘flush.console’
metahdep.format: no visible global function definition for ‘new’
new.LinMod.HBLM.fast.dep.delta.split: no visible global function
  definition for ‘pnorm’
Undefined global functions or variables:
  annotation coefs fitPLM flush.console new pchisq pnorm pt sd varcov
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "pchisq", "pnorm", "pt", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: metahdep.other.Rd:40-42: Dropping empty section \usage
prepare_Rd: metahdep.other.Rd:43-45: Dropping empty section \arguments
prepare_Rd: metahdep.other.Rd:46-48: Dropping empty section \value
* 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
* 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: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/metahdep.Rcheck/00check.log’
for details.



Installation output

metahdep.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL metahdep
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘metahdep’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c metahdep.c -o metahdep.o
metahdep.c:471:79: warning: incompatible pointer to integer conversion passing 'const char *' to parameter of type 'char' [-Wint-conversion]
                                index = metan_binary_search_unique(name_list, sort_index, R_old_names, j, CHAR(STRING_ELT(R_old_chipsets, j)), i);
                                                                                                          ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:478:18: note: expanded from macro 'CHAR'
#define CHAR(x)         R_CHAR(x)
                        ^˜˜˜˜˜˜˜˜
metahdep.c:372:103: note: passing argument to parameter 'chipset_name' here
SEXP metan_binary_search_unique(SEXP name_list, SEXP sort_index, SEXP gene_name, int gene_index, char chipset_name, int study_num)
                                                                                                      ^
1 warning generated.
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 metahdep.so metahdep.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/metahdep/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
* DONE (metahdep)

Tests output


Example timings

metahdep.Rcheck/metahdep-Ex.timings

nameusersystemelapsed
ES.obj-class0.0290.0040.034
HGU.DifExp.list0.0120.0060.017
HGU.newnames0.0660.0070.073
HGU.prep.list0.0310.0040.034
getPLM.es0.0010.0000.001
gloss0.0060.0020.008
metahdep.FEMA0.0350.0060.045
metahdep.HBLM0.7450.0370.793
metahdep1.4410.0311.483
metahdep.REMA0.0680.0080.076
metahdep.format0.1860.0110.199
metahdep.other0.0020.0000.002
metaprep-class0.0240.0040.027