##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:rhdf5.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings rhdf5_2.38.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/rhdf5.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rhdf5/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5’ version ‘2.38.1’
* 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 ‘rhdf5’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
* 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 ... 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 shell scripts ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.14-bioc/R/library/rhdf5/libs/rhdf5.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

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 ... OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/rhdf5.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL rhdf5
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘rhdf5’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/external_filters.h
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5.c -o H5.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5A.c -o H5A.o
H5A.c: In function ‘H5Aread_helper_STRING’:
H5A.c:245:12: warning: unused variable ‘herr’ [-Wunused-variable]
  245 |     herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
      |            ^~~~
H5A.c: In function ‘H5Aread_helper_INTEGER’:
H5A.c:206:9: warning: ‘Rval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  206 |   return(Rval);
      |         ^
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5D.c -o H5D.o
H5D.c: In function ‘H5Dread_helper_INTEGER’:
H5D.c:154:20: warning: unused variable ‘status’ [-Wunused-variable]
  154 |             herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
      |                    ^~~~~~
H5D.c:151:18: warning: unused variable ‘status’ [-Wunused-variable]
  151 |           herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_UCHAR);
      |                  ^~~~~~
H5D.c:183:20: warning: unused variable ‘status’ [-Wunused-variable]
  183 |             herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
      |                    ^~~~~~
H5D.c:180:18: warning: unused variable ‘status’ [-Wunused-variable]
  180 |           herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
      |                  ^~~~~~
H5D.c:216:24: warning: unused variable ‘status’ [-Wunused-variable]
  216 |                 herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
      |                        ^~~~~~
H5D.c:213:20: warning: unused variable ‘status’ [-Wunused-variable]
  213 |             herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
      |                    ^~~~~~
H5D.c:265:24: warning: unused variable ‘status’ [-Wunused-variable]
  265 |                 herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
      |                        ^~~~~~
H5D.c:262:20: warning: unused variable ‘status’ [-Wunused-variable]
  262 |             herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative);
      |                    ^~~~~~
H5D.c: In function ‘H5Dread_helper_FLOAT’:
H5D.c:358:20: warning: unused variable ‘status’ [-Wunused-variable]
  358 |             herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
      |                    ^~~~~~
H5D.c:355:16: warning: unused variable ‘status’ [-Wunused-variable]
  355 |         herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE);
      |                ^~~~~~
H5D.c: In function ‘H5Dread_helper_ENUM’:
H5D.c:466:20: warning: unused variable ‘status’ [-Wunused-variable]
  466 |             herr_t status = H5Tenum_insert (enumtype, st, &i);
      |                    ^~~~~~
H5D.c:476:24: warning: unused variable ‘status’ [-Wunused-variable]
  476 |                 herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
      |                        ^~~~~~
H5D.c:473:20: warning: unused variable ‘status’ [-Wunused-variable]
  473 |             herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype);
      |                    ^~~~~~
H5D.c: In function ‘H5Dread_helper_ARRAY’:
H5D.c:554:24: warning: unused variable ‘status’ [-Wunused-variable]
  554 |                 herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
      |                        ^~~~~~
H5D.c:551:20: warning: unused variable ‘status’ [-Wunused-variable]
  551 |             herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype);
      |                    ^~~~~~
H5D.c: In function ‘H5Dread_helper_COMPOUND’:
H5D.c:660:11: warning: unused variable ‘mem_type_id’ [-Wunused-variable]
  660 |     hid_t mem_type_id = -1;
      |           ^~~~~~~~~~~
H5D.c: In function ‘H5Dread_helper’:
H5D.c:782:12: warning: unused variable ‘status’ [-Wunused-variable]
  782 |     herr_t status = H5Tclose(dtype_id);
      |            ^~~~~~
H5D.c: In function ‘H5Dread_helper_INTEGER’:
H5D.c:318:21: warning: ‘intbuf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  318 |                     int64_to_integer64(intbuf, n, buf, sgn);
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:264:38: warning: ‘dtypeNative’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  264 |                 hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(dtypeNative));
      |                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c: In function ‘H5Dread_helper_ARRAY’:
H5D.c:576:23: warning: ‘buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  576 |         herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:610:39: warning: ‘Rval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  610 |                 INTEGER(buffer)[li] = INTEGER(Rval)[lj];
      |                                       ^~~~~~~~~~~~~
H5D.c:553:38: warning: ‘arraytype’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  553 |                 hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(arraytype));
      |                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5E.c -o H5E.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/include/R.h:75,
                 from H5E.h:4,
                 from H5E.c:1:
H5E.c: In function ‘custom_print_cb’:
/home/biocbuild/bbs-3.14-bioc/R/include/R_ext/Error.h:52:15: warning: label ‘Rf_error’ defined but not used [-Wunused-label]
   52 | #define error Rf_error
      |               ^~~~~~~~
H5E.c:66:5: note: in expansion of macro ‘error’
   66 |     error:
      |     ^~~~~
H5E.c: In function ‘custom_print_cb_compact’:
/home/biocbuild/bbs-3.14-bioc/R/include/R_ext/Error.h:52:15: warning: label ‘Rf_error’ defined but not used [-Wunused-label]
   52 | #define error Rf_error
      |               ^~~~~~~~
H5E.c:98:5: note: in expansion of macro ‘error’
   98 |     error:
      |     ^~~~~
H5E.c:75:15: warning: unused variable ‘indent’ [-Wunused-variable]
   75 |     const int indent = 4;
      |               ^~~~~~
H5E.c: In function ‘_rhdf5PrintErrorR’:
H5E.c:110:16: warning: unused variable ‘eee’ [-Wunused-variable]
  110 |         herr_t eee = H5Ewalk(estack_id_copy, H5E_WALK_DOWNWARD, &custom_print_cb, &client_data);
      |                ^~~
H5E.c: In function ‘_rhdf5PrintErrorRcompact’:
H5E.c:141:16: warning: unused variable ‘eee’ [-Wunused-variable]
  141 |         herr_t eee = H5Ewalk(estack_id_copy, H5E_WALK_DOWNWARD, &custom_print_cb_compact, &client_data);
      |                ^~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5F.c -o H5F.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5G.c -o H5G.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5I.c -o H5I.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5L.c -o H5L.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5O.c -o H5O.o
H5O.c: In function ‘H5Oget_num_attrs’:
H5O.c:13:10: warning: unused variable ‘herr’ [-Wunused-variable]
   13 |   herr_t herr = H5Aiterate( obj_id, H5_INDEX_CRT_ORDER, H5_ITER_NATIVE, &idx, &opAcount, &n);
      |          ^~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5P.c -o H5P.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5S.c -o H5S.o
H5S.c: In function ‘_H5Sselect_hyperslab’:
H5S.c:258:12: warning: unused variable ‘herr’ [-Wunused-variable]
  258 |     herr_t herr = H5Sselect_hyperslab( space_id, op, start, stride, count, block );
      |            ^~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5S_extras.c -o H5S_extras.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5T.c -o H5T.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5Z.c -o H5Z.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c H5constants.c -o H5constants.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c HandleList.cpp -o HandleList.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c HandleListWrap.c -o HandleListWrap.o
HandleListWrap.c: In function ‘_h5listOpenObjects’:
HandleListWrap.c:138:12: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
  138 |     herr_t status;
      |            ^~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bit64conversion.c -o bit64conversion.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c external_filters.c -o external_filters.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5dump.c -o h5dump.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5ls.c -o h5ls.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5testLock.c -o h5testLock.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c printdatatype.c -o printdatatype.o
printdatatype.c: In function ‘getDatatypeName’:
printdatatype.c:21:16: warning: variable ‘sign_s’ set but not used [-Wunused-but-set-variable]
   21 |   const char  *sign_s=NULL;   /* sign scheme string */
      |                ^~~~~~
printdatatype.c:19:16: warning: variable ‘order_s’ set but not used [-Wunused-but-set-variable]
   19 |   const char  *order_s=NULL;  /* byte order string */
      |                ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c wrap.c -o wrap.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-rhdf5/00new/rhdf5/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** 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 (rhdf5)

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(rhdf5)
> 
> test_check("rhdf5")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 923 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (2)

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 923 ]
> 
> proc.time()
   user  system elapsed 
  6.043   2.291   8.329