Back to Long Tests report for BioC 3.10

CHECK report for HDF5Array on malbec1

This page was generated on 2019-11-30 19:30:03 -0500 (Sat, 30 Nov 2019).

Package 4/4HostnameOS / ArchCHECK
HDF5Array 1.14.0
Hervé Pagès
Snapshot Date: 2019-11-30 10:00:01 -0500 (Sat, 30 Nov 2019)
URL: https://git.bioconductor.org/packages/HDF5Array
Branch: RELEASE_3_10
Last Commit: ab16f71
Last Changed Date: 2019-11-27 02:09:40 -0500 (Wed, 27 Nov 2019)
malbec1 Linux (Ubuntu 18.04.3 LTS) / x86_64 [ ERROR ]

Summary

Package: HDF5Array
Version: 1.14.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no HDF5Array_1.14.0.tar.gz
StartedAt: 2019-11-30 11:00:21 -0500 (Sat, 30 Nov 2019)
EndedAt: 2019-11-30 11:01:26 -0500 (Sat, 30 Nov 2019)
EllapsedTime: 65.4 seconds
RetCode: 1
Status:  ERROR 
CheckDir: HDF5Array.Rcheck
Warnings: NA

Tests output

HDF5Array.Rcheck/tests/fake_test1.Rout.fail


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.

> cat("This fake test doesn't test anything...\n")
This fake test doesn't test anything...
> 
> stop("... and FAILS!\n")
Error: ... and FAILS!
Execution halted

HDF5Array.Rcheck/tests/fake_test2.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.

> cat("This fake test doesn't test anything...\n")
This fake test doesn't test anything...
> 
> cat("... and succeeds.\n")
... and succeeds.
> 
> 
> proc.time()
   user  system elapsed 
  0.136   0.032   0.167 

HDF5Array.Rcheck/tests/fake_test3.Rout.fail


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.

> cat("This fake test doesn't test anything...\n")
This fake test doesn't test anything...
> 
> stop("... and FAILS!\n")
Error: ... and FAILS!
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no HDF5Array_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc-longtests/meat/HDF5Array.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.14.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HDF5Array’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.2Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
    libs     14.7Mb
* 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
* 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’ ‘S4Vectors:::anyMissingOrOutside’
  ‘S4Vectors:::extract_data_frame_rows’ ‘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 ... OK
* checking for code/documentation mismatches ... SKIPPED
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘fake_test1.R’
  Running ‘fake_test2.R’
  Running ‘fake_test3.R’
 ERROR
Running the tests in ‘longtests/fake_test1.R’ failed.
Complete output:
  > cat("This fake test doesn't test anything...\n")
  This fake test doesn't test anything...
  > 
  > stop("... and FAILS!\n")
  Error: ... and FAILS!
  Execution halted
Running the tests in ‘longtests/fake_test3.R’ failed.
Complete output:
  > cat("This fake test doesn't test anything...\n")
  This fake test doesn't test anything...
  > 
  > stop("... and FAILS!\n")
  Error: ... and FAILS!
  Execution halted
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc-longtests/meat/HDF5Array.Rcheck/00check.log’
for details.


Installation output

HDF5Array.Rcheck/00install.out

* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c DSetHandle.c -o DSetHandle.o
DSetHandle.c: In function ‘_get_DSetHandle’:
DSetHandle.c:100:6: warning: ‘storage_mode_attr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (strcmp(storage_mode, "integer") == 0) {
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DSetHandle.c:220:8: note: ‘storage_mode_attr’ was declared here
  char *storage_mode_attr;
        ^~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_init_HDF5Array.c -o R_init_HDF5Array.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c array_selection.c -o array_selection.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c h5mread.c -o h5mread.o
h5mread.c:1213:22: warning: ‘select_elements_from_chunk’ defined but not used [-Wunused-function]
 static long long int select_elements_from_chunk(const DSetHandle *dset_handle,
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o HDF5Array.so DSetHandle.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5mread.o /home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.10-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc-longtests/meat/HDF5Array.Rcheck/00LOCK-HDF5Array/00new/HDF5Array/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HDF5Array)