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CHECK report for rhdf5client on tokay2

This page was generated on 2018-10-17 08:44:48 -0400 (Wed, 17 Oct 2018).

Package 1237/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rhdf5client 1.2.3
Samuela Pollack
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/rhdf5client
Branch: RELEASE_3_7
Last Commit: 873d846
Last Changed Date: 2018-09-28 14:42:46 -0400 (Fri, 28 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: rhdf5client
Version: 1.2.3
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rhdf5client.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings rhdf5client_1.2.3.tar.gz
StartedAt: 2018-10-17 04:25:32 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:27:50 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 138.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: rhdf5client.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rhdf5client.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings rhdf5client_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/rhdf5client.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rhdf5client/DESCRIPTION' ... OK
* this is package 'rhdf5client' version '1.2.3'
* 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 'rhdf5client' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 ... OK
* 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 ... WARNING
Rd files with duplicated alias 'H5S_dataset,[,character,character-method':
  'sub-H5S_dataset-character-character-ANY-method.Rd'
  'sub-H5S_dataset-character-character-method.Rd'
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'H5S_dataset,numeric,numeric'
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: 2 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/rhdf5client.Rcheck/00check.log'
for details.



Installation output

rhdf5client.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/rhdf5client_1.2.3.tar.gz && rm -rf rhdf5client.buildbin-libdir && mkdir rhdf5client.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rhdf5client.buildbin-libdir rhdf5client_1.2.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL rhdf5client_1.2.3.zip && rm rhdf5client_1.2.3.tar.gz rhdf5client_1.2.3.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  286k  100  286k    0     0  3782k      0 --:--:-- --:--:-- --:--:-- 4207k

install for i386

* installing *source* package 'rhdf5client' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rhdf5client'
    finding HTML links ... done
    H5S_Array-class                         html  
    H5S_Array                               html  
    H5S_ArraySeed-class                     html  
    H5S_Matrix-class                        html  
    H5S_dataset-class                       html  
    H5S_dataset2                            html  
    H5S_source-class                        html  
    HSDS_Matrix                             html  
    URL_h5serv                              html  
    URL_hsds                                html  
    dim-H5S_ArraySeed-method                html  
    dimnames-H5S_ArraySeed-method           html  
    domains-method                          html  
    dsmeta                                  html  
    extract-methods                         html  
    getDatasetAttrs                         html  
    getDatasetSlice                         html  
    getDatasetUUIDs                         html  
    getDims                                 html  
    getHRDF                                 html  
    getReq                                  html  
    groups-H5S_source-missing-method        html  
    groups-H5S_source-numeric-method        html  
    hsdsInfo-method                         html  
    internalDim                             html  
    links                                   html  
    setPath-methods                         html  
    sproc                                   html  
    sub-H5S_dataset-character-character-ANY-method
                                            html  
    sub-H5S_dataset-character-character-method
                                            html  
    targets                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'rhdf5client' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rhdf5client' as rhdf5client_1.2.3.zip
* DONE (rhdf5client)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'rhdf5client' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

rhdf5client.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(rhdf5client)
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

> 
> test_check("rhdf5client")
== testthat results  ===========================================================
OK: 16 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.07    0.21   10.40 

rhdf5client.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(rhdf5client)
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

> 
> test_check("rhdf5client")
== testthat results  ===========================================================
OK: 16 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.62    0.23   10.56 

Example timings

rhdf5client.Rcheck/examples_i386/rhdf5client-Ex.timings

nameusersystemelapsed
H5S_Array0.280.041.55
H5S_dataset20.120.000.92
H5S_source-class0.170.000.98
HSDS_Matrix000
URL_h5serv000
URL_hsds0.020.000.02
domains-method0.030.000.34
dsmeta0.120.000.75
getDatasetAttrs0.030.000.47
getDatasetSlice0.020.000.45
getDatasetUUIDs0.030.000.68
getDims0.100.000.51
getHRDF0.010.020.47
groups-H5S_source-missing-method0.140.020.92
hsdsInfo-method0.030.000.35
internalDim0.140.001.07
links0.100.000.97
setPath-methods0.000.020.22
sproc000
targets0.110.010.93

rhdf5client.Rcheck/examples_x64/rhdf5client-Ex.timings

nameusersystemelapsed
H5S_Array0.330.011.50
H5S_dataset20.070.000.85
H5S_source-class0.170.000.99
HSDS_Matrix000
URL_h5serv000
URL_hsds000
domains-method0.020.000.36
dsmeta0.140.000.74
getDatasetAttrs0.050.000.46
getDatasetSlice0.040.000.48
getDatasetUUIDs0.050.000.67
getDims0.050.000.47
getHRDF0.060.020.50
groups-H5S_source-missing-method0.270.001.30
hsdsInfo-method0.040.000.37
internalDim0.190.001.44
links0.160.020.95
setPath-methods0.010.000.25
sproc0.020.000.02
targets0.150.000.94