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BioC 3.4: CHECK report for HDF5Array on moscato1

This page was generated on 2016-09-21 03:48:05 -0700 (Wed, 21 Sep 2016).

Package 567/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HDF5Array 1.1.13
Hervé Pagès
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HDF5Array
Last Changed Rev: 119369 / Revision: 121152
Last Changed Date: 2016-07-14 10:50:32 -0700 (Thu, 14 Jul 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: HDF5Array
Version: 1.1.13
Command: rm -rf HDF5Array.buildbin-libdir HDF5Array.Rcheck && mkdir HDF5Array.buildbin-libdir HDF5Array.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HDF5Array.buildbin-libdir HDF5Array_1.1.13.tar.gz >HDF5Array.Rcheck\00install.out 2>&1 && cp HDF5Array.Rcheck\00install.out HDF5Array-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=HDF5Array.buildbin-libdir --install="check:HDF5Array-install.out" --force-multiarch --no-vignettes --timings HDF5Array_1.1.13.tar.gz
StartedAt: 2016-09-20 10:19:20 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:31:16 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 715.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: HDF5Array.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf HDF5Array.buildbin-libdir HDF5Array.Rcheck && mkdir HDF5Array.buildbin-libdir HDF5Array.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HDF5Array.buildbin-libdir HDF5Array_1.1.13.tar.gz >HDF5Array.Rcheck\00install.out 2>&1 && cp HDF5Array.Rcheck\00install.out HDF5Array-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=HDF5Array.buildbin-libdir --install="check:HDF5Array-install.out" --force-multiarch --no-vignettes --timings HDF5Array_1.1.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/HDF5Array.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HDF5Array/DESCRIPTION' ... OK
* this is package 'HDF5Array' version '1.1.13'
* package encoding: UTF-8
* 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 whether package 'HDF5Array' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Unexported objects imported by ':::' calls:
  'BiocGenerics:::testPackage' 'IRanges:::combine_dimnames'
  'IRanges:::combine_dimnames_along' 'IRanges:::combine_dims_along'
  'IRanges:::get_dims_to_bind' 'IRanges:::simple_abind'
  'S4Vectors:::anyMissingOrOutside' 'S4Vectors:::sapply_isNULL'
  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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'dlogis' and siglist 'DelayedArray'
  generic 'plogis' and siglist 'DelayedArray'
  generic 'qlogis' and siglist 'DelayedArray'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
HDF5Array-class 4.31   0.74    5.79
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/HDF5Array.Rcheck/00check.log'
for details.


HDF5Array.Rcheck/00install.out:


install for i386

* installing *source* package 'HDF5Array' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'as.array' from package 'base' in package 'HDF5Array'
Creating a new generic function for 'apply' in package 'HDF5Array'
Creating a generic function for 'dlogis' from package 'stats' in package 'HDF5Array'
Creating a generic function for 'plogis' from package 'stats' in package 'HDF5Array'
Creating a generic function for 'qlogis' from package 'stats' in package 'HDF5Array'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'HDF5Array' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HDF5Array' as HDF5Array_1.1.13.zip
* DONE (HDF5Array)

HDF5Array.Rcheck/examples_i386/HDF5Array-Ex.timings:

nameusersystemelapsed
DelayedArray-class2.770.083.66
DelayedArray-utils2.300.252.55
HDF5Array-class3.930.584.76
cbind-methods0.940.040.98
setHDF5DumpFile0.590.050.64

HDF5Array.Rcheck/examples_x64/HDF5Array-Ex.timings:

nameusersystemelapsed
DelayedArray-class2.690.143.27
DelayedArray-utils2.270.282.61
HDF5Array-class4.310.745.79
cbind-methods0.900.141.04
setHDF5DumpFile0.780.062.03