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BioC 3.5: CHECK report for metahdep on malbec2

This page was generated on 2017-08-16 13:13:18 -0400 (Wed, 16 Aug 2017).

Package 793/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metahdep 1.34.0
John R. Stevens
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/metahdep
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: metahdep
Version: 1.34.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings metahdep_1.34.0.tar.gz
StartedAt: 2017-08-16 00:28:03 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:28:27 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 24.0 seconds
RetCode: 0
Status:  OK 
CheckDir: metahdep.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings metahdep_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/metahdep.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.34.0’
* 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 ... 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 loading without being on the library search path ... 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 ... OK
* checking installed files from ‘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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/metahdep.Rcheck/00check.log’
for details.


metahdep.Rcheck/00install.out:

* installing *source* package ‘metahdep’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c metahdep.c -o metahdep.o
In file included from metahdep.c:3:0:
metahdep.c: In function ‘get_row_indices2’:
/home/biocbuild/bbs-3.5-bioc/R/include/Rinternals.h:463:18: warning: passing argument 5 of ‘metan_binary_search_unique’ makes integer from pointer without a cast [-Wint-conversion]
 #define CHAR(x)  R_CHAR(x)
                  ^
metahdep.c:471:79: note: in expansion of macro ‘CHAR’
     index = metan_binary_search_unique(name_list, sort_index, R_old_names, j, CHAR(STRING_ELT(R_old_chipsets, j)), i);
                                                                               ^
metahdep.c:372:6: note: expected ‘char’ but argument is of type ‘const char *’
 SEXP metan_binary_search_unique(SEXP name_list, SEXP sort_index, SEXP gene_name, int gene_index, char chipset_name, int study_num)
      ^
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o metahdep.so metahdep.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/metahdep.Rcheck/metahdep/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metahdep)

metahdep.Rcheck/metahdep-Ex.timings:

nameusersystemelapsed
ES.obj-class0.0200.0080.026
HGU.DifExp.list0.0080.0000.009
HGU.newnames0.060.000.06
HGU.prep.list0.0400.0000.039
getPLM.es0.0000.0000.001
gloss0.0040.0000.003
metahdep.FEMA0.0960.0000.098
metahdep.HBLM0.5760.0000.579
metahdep1.2360.0201.258
metahdep.REMA0.0680.0120.080
metahdep.format0.1600.0200.182
metahdep.other0.0000.0000.002
metaprep-class0.0240.0080.032