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This page was generated on 2022-04-13 12:05:51 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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INSTALL results for rhdf5 on nebbiolo2


To the developers/maintainers of the rhdf5 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rhdf5.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
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raw results

Package 1598/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rhdf5 2.38.1  (landing page)
Mike Smith
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/rhdf5
git_branch: RELEASE_3_14
git_last_commit: 1a5587e
git_last_commit_date: 2022-03-09 08:07:18 -0400 (Wed, 09 Mar 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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: rhdf5
Version: 2.38.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL rhdf5
StartedAt: 2022-04-12 03:18:05 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 03:18:16 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 11.2 seconds
RetCode: 0
Status:   OK  

Command output

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