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CHECK report for rhdf5client on malbec1

This page was generated on 2019-04-16 11:53:07 -0400 (Tue, 16 Apr 2019).

Package 1306/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rhdf5client 1.4.1
Samuela Pollack
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/rhdf5client
Branch: RELEASE_3_8
Last Commit: 939791a
Last Changed Date: 2018-12-14 12:44:21 -0400 (Fri, 14 Dec 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: rhdf5client
Version: 1.4.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:rhdf5client.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings rhdf5client_1.4.1.tar.gz
StartedAt: 2019-04-16 02:37:26 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:39:19 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 113.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: rhdf5client.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:rhdf5client.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings rhdf5client_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/rhdf5client.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rhdf5client/DESCRIPTION’ ... OK
* this is package ‘rhdf5client’ version ‘1.4.1’
* 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 for sufficient/correct file permissions ... 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
* 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getDataList’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
HSDS_Matrix: warning in readBin(GET(targ)$content, w = "character"):
  partial argument match of 'w' to 'what'
* 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 ... WARNING
Duplicated \argument entries in documentation object 'dim':
  ‘x’

Duplicated \argument entries in documentation object 'dimnames,H5S_ArraySeed-method':
  ‘x’

Duplicated \argument entries in documentation object '[,H5S_dataset,numeric,numeric-method':
  ‘x’ ‘i’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
listDomains-methods 0.072      0  10.457
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/rhdf5client.Rcheck/00check.log’
for details.



Installation output

rhdf5client.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL rhdf5client
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘rhdf5client’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c extract.c -o extract.o
extract.c: In function ‘extractBin’:
extract.c:101:42: warning: ‘rdp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     A[ia] = (Rf_isReal(resvec_sexp) ? rdp[ib] : rip[ib]);
                                          ^
extract.c:101:52: warning: ‘rip’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     A[ia] = (Rf_isReal(resvec_sexp) ? rdp[ib] : rip[ib]);
                                                    ^
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o rhdf5client.so extract.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/rhdf5client/libs
** R
** inst
** 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 (rhdf5client)

Tests output

rhdf5client.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
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: 19 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 13.444   3.284  23.973 

Example timings

rhdf5client.Rcheck/rhdf5client-Ex.timings

nameusersystemelapsed
H5S_Array0.0000.0000.001
H5S_dataset20.2760.0160.987
H5S_source-class0.1240.0040.763
HSDSDataset0.1760.0041.086
HSDSFile0.0240.0000.272
HSDSSource0.0000.0000.001
HSDS_Matrix0.4000.0121.282
HSDS_Matrix_OLD0.0000.0000.001
URL_h5serv000
URL_hsds000
domains0.0400.0000.559
dsmeta000
fetchDatasets0.0440.0040.414
getData-methods0.1440.0161.439
getDatasetAttrs0.0560.0040.496
getDatasetSlice0.0280.0080.373
getDatasetUUIDs0.0280.0000.282
getDims0.0160.0080.280
getHRDF0.0640.0040.525
groups-methods000
hsdsInfo0.0200.0120.289
internalDim000
links000
listDatasets0.0680.0040.898
listDomains-methods 0.072 0.00010.457
setPath0.0160.0000.189
sproc0.0040.0000.003
targets0.0000.0000.001