| Back to Long Tests report for BioC 3.10 |
This page was generated on 2020-04-11 19:30:02 -0400 (Sat, 11 Apr 2020).
| Package 4/4 | Hostname | OS / Arch | CHECK | |||||
| HDF5Array 1.14.3 Hervé Pagès
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | [ ERROR ] |
| Package: HDF5Array |
| Version: 1.14.3 |
| 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_1.14.3.tar.gz |
| StartedAt: 2020-04-11 11:00:16 -0400 (Sat, 11 Apr 2020) |
| EndedAt: 2020-04-11 11:01:21 -0400 (Sat, 11 Apr 2020) |
| EllapsedTime: 64.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: HDF5Array.Rcheck |
| Warnings: NA |
HDF5Array.Rcheck/tests/fake_test1.Rout.fail
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
0.132 0.012 0.144
HDF5Array.Rcheck/tests/fake_test3.Rout.fail
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
##############################################################################
##############################################################################
###
### 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_1.14.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc-longtests/meat/HDF5Array.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.14.3’
* 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.
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:236:8: 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)