Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2021-10-15 15:06:19 -0400 (Fri, 15 Oct 2021).

CHECK results for rhdf5client on tokay2

To the developers/maintainers of the rhdf5client package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rhdf5client.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1574/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rhdf5client 1.14.2  (landing page)
Vincent Carey
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/rhdf5client
git_branch: RELEASE_3_13
git_last_commit: a24e7d8
git_last_commit_date: 2021-06-23 16:43:25 -0400 (Wed, 23 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: rhdf5client
Version: 1.14.2
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rhdf5client.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings rhdf5client_1.14.2.tar.gz
StartedAt: 2021-10-15 04:32:09 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 04:35:32 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 203.6 seconds
RetCode: 0
Status:   OK  
CheckDir: rhdf5client.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rhdf5client.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings rhdf5client_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/rhdf5client.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.14.2'
* 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 '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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/rhdf5client/libs/i386/rhdf5client.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/rhdf5client/libs/x64/rhdf5client.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
listDomains-methods 0.04      0   10.57
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
listDomains-methods 0.02      0    10.5
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/rhdf5client.Rcheck/00check.log'
for details.



Installation output

rhdf5client.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/rhdf5client_1.14.2.tar.gz && rm -rf rhdf5client.buildbin-libdir && mkdir rhdf5client.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rhdf5client.buildbin-libdir rhdf5client_1.14.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL rhdf5client_1.14.2.zip && rm rhdf5client_1.14.2.tar.gz rhdf5client_1.14.2.zip
###
##############################################################################
##############################################################################


  % 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  301k  100  301k    0     0   983k      0 --:--:-- --:--:-- --:--:--  985k

install for i386

* installing *source* package 'rhdf5client' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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]);
                                                    ^
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o rhdf5client.dll tmp.def extract.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/rhdf5client.buildbin-libdir/00LOCK-rhdf5client/00new/rhdf5client/libs/i386
** 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                             html  
    H5S_dataset2                            html  
    H5S_source-class                        html  
    HSDSArray                               html  
    HSDSArraySeed                           html  
    HSDSDataset-class                       html  
    HSDSDataset                             html  
    HSDSFile-class                          html  
    HSDSFile                                html  
    HSDSMatrix                              html  
    HSDSSource-class                        html  
    HSDSSource                              html  
    HSDS_Matrix                             html  
    HSDS_Matrix_OLD                         html  
    URL_h5serv                              html  
    URL_hsds                                html  
    as                                      html  
    check_hsds                              html  
    dataset                                 html  
    dim-H5S_ArraySeed-method                html  
    dim                                     html  
    dimnames-H5S_ArraySeed-method           html  
    dimnames                                html  
    domains                                 html  
    dsmeta                                  html  
    extract_array                           html  
    fetchDatasets                           html  
    getData-methods                         html  
    getDatasetAttrs                         html  
    getDatasetSlice                         html  
    getDatasetUUIDs                         html  
    getDims                                 html  
    getHRDF                                 html  
    getReq                                  html  
    groups-methods                          html  
    hsdsInfo                                html  
    internalDim                             html  
    links                                   html  
    listDatasets                            html  
    listDomains-methods                     html  
    rhdf5client-deprecated                  html  
    rhdf5client                             html  
    setPath                                 html  
    sproc                                   html  
    sub-H5S_dataset-character-character-ANY-method
                                            html  
    sub-H5S_dataset-numeric-numeric-ANY-method
                                            html  
    sub-HSDSDataset-numeric-ANY-ANY-method
                                            html  
    sub-HSDSDataset-numeric-numeric-ANY-method
                                            html  
    sub-sub                                 html  
    targets                                 html  
    transfermode                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'rhdf5client' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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]);
                                                    ^
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o rhdf5client.dll tmp.def extract.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/rhdf5client.buildbin-libdir/rhdf5client/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rhdf5client' as rhdf5client_1.14.2.zip
* DONE (rhdf5client)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'rhdf5client' successfully unpacked and MD5 sums checked

Tests output

rhdf5client.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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: Matrix
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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand, unname

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep

> 
> test_check("rhdf5client")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  11.70    0.40   17.12 

rhdf5client.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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: Matrix
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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand, unname

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep

> 
> test_check("rhdf5client")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  16.07    2.14   23.11 

Example timings

rhdf5client.Rcheck/examples_i386/rhdf5client-Ex.timings

nameusersystemelapsed
H5S_Array000
H5S_dataset2000
H5S_source-class000
HSDSArray0.280.022.11
HSDSDataset0.030.000.78
HSDSFile0.030.000.46
HSDSSource0.000.000.11
HSDS_Matrix000
HSDS_Matrix_OLD000
URL_h5serv000
URL_hsds000
domains000
dsmeta000
fetchDatasets000
getData-methods0.220.032.48
getDatasetAttrs000
getDatasetSlice000
getDatasetUUIDs000
getDims000
getHRDF000
groups-methods000
hsdsInfo000
internalDim000
links000
listDatasets0.050.000.46
listDomains-methods 0.04 0.0010.57
setPath000
sproc000
targets000

rhdf5client.Rcheck/examples_x64/rhdf5client-Ex.timings

nameusersystemelapsed
H5S_Array000
H5S_dataset2000
H5S_source-class000
HSDSArray0.180.001.24
HSDSDataset0.040.020.57
HSDSFile0.030.000.46
HSDSSource0.030.000.12
HSDS_Matrix000
HSDS_Matrix_OLD000
URL_h5serv000
URL_hsds000
domains000
dsmeta000
fetchDatasets000
getData-methods0.240.032.08
getDatasetAttrs000
getDatasetSlice000
getDatasetUUIDs000
getDims000
getHRDF000
groups-methods000
hsdsInfo000
internalDim000
links000
listDatasets0.030.000.45
listDomains-methods 0.02 0.0010.50
setPath000
sproc000
targets000