{bio}[foss/2021a] CellProfiler v4.2.4, mysqlclient v2.1.1 w/ Python 3.9.5

[boegel]

(created using eb --new-pr)

[boegel]

@boegelbot please test @ generoso

[boegelbot]

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=16489 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_16489 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

• exit code: 0
• output:

Submitted batch job 9373

Test results coming soon (I hope)...

- notification for comment with ID 1291021284 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegel]

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3106.skitty.os - Linux RHEL 8.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/be0860a20927c3c772d9fd36cf8b8921 for a full test report.

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
cns8 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/2a5e9554ab2e8ea672b5dbd10720b069 for a full test report.

[boegel]

@boegelbot please test @ jsc-zen2

[boegelbot]

@boegel: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=16489 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_16489 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

• exit code: 0
• output:

Submitted batch job 1729

Test results coming soon (I hope)...

- notification for comment with ID 1291630449 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegelbot]

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (2 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/1e8f26c1d97204ded9428e2d58d73871 for a full test report.

[verdurin]

@boegel Seeing a problem building deep libsoup here on one node (will try elsewhere in the meantime):

== 2022-10-31 16:09:59,904 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): cmd " ni
nja -j 8 " exited with exit code 1 and output:
[1/182] Compiling C object subprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p/sysprof-address.c.o
[2/182] Compiling C object subprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p/sysprof-capture-util.c.o
[3/182] Compiling C object subprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p/sysprof-capture-cursor.c.o
FAILED: subprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p/sysprof-capture-cursor.c.o
gcc -Isubprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p -Isubprojects/sysprof/src/libsysprof-capture -I../libsoup-2.74.0/su
bprojects/sysprof/src/libsysprof-capture -I/eb/maint/software/cURL/7.76.0-GCCcore-10.3.0/include -I/eb/maint/software/libpsl/0.21.1-GCCcore-1
0.3.0/include -I/eb/maint/software/GLib/2.68.2-GCCcore-10.3.0/include -I/eb/maint/software/SQLite/3.35.4-GCCcore-10.3.0/include -I/eb/maint/s
oftware/libxml2/2.9.10-GCCcore-10.3.0/include -I/eb/maint/software/GObject-Introspection/1.68.0-GCCcore-10.3.0/include -I/eb/maint/software/b
inutils/2.36.1-GCCcore-10.3.0/include -I/dev/shm/LibSoup/2.74.0/GCCcore-10.3.0/easybuild_obj -fvisibility=hidden -fdiagnostics-color=always -
D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -std=c99 -g -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -Wcast-align -Wdeclaration-after-statem
ent -Wformat-nonliteral -Wformat-security -Wmissing-include-dirs -Wnested-externs -Wno-missing-field-initializers -Wno-sign-compare -Wno-unus
ed-parameter -Wno-cast-function-type -Wpointer-arith -Wredundant-decls -Wswitch-default -Wswitch-enum -Wuninitialized -Werror=format-security
 -Werror=format=2 -Werror=empty-body -Werror=implicit-function-declaration -Werror=incompatible-pointer-types -Werror=pointer-arith -Werror=i
nit-self -Werror=int-conversion -Werror=misleading-indentation -Werror=missing-include-dirs -Werror=overflow -Werror=return-type -Werror=shad
ow -Werror=strict-prototypes -Werror=undef -fstack-protector-strong -O2 -ftree-vectorize -march=native -fno-math-errno -std=gnu11 -fPIC -pthr
ead -DSYSPROF_CAPTURE_COMPILATION -MD -MQ subprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p/sysprof-capture-cursor.c.o -MF
subprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p/sysprof-capture-cursor.c.o.d -o subprojects/sysprof/src/libsysprof-captur
e/libsysprof-capture-4.a.p/sysprof-capture-cursor.c.o -c ../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-cursor.
c
../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-cursor.c: In function sysprof_capture_cursor_add_condition:
../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-cursor.c:296:22: error: implicit declaration of function reallocarray [-Werror=implicit-function-declaration]
  296 |   self->conditions = reallocarray (self->conditions, ++self->n_conditions, sizeof (*self->conditions));
      |                      ^~~~~~~~~~~~
../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-cursor.c:296:22: warning: nested extern declaration of reallocarray [-Wnested-externs]
../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-cursor.c:296:20: error: assignment to SysprofCaptureCondition ** {aka struct _SysprofCaptureCondition **} from int makes pointer from integer without a cast [-Werror=int-conversion]
  296 |   self->conditions = reallocarray (self->conditions, ++self->n_conditions, sizeof (*self->conditions));
      |                    ^
cc1: some warnings being treated as errors
[4/182] Compiling C object subprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p/sysprof-capture-writer-cat.c.o
FAILED: subprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p/sysprof-capture-writer-cat.c.o
gcc -Isubprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p -Isubprojects/sysprof/src/libsysprof-capture -I../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture -I/eb/maint/software/cURL/7.76.0-GCCcore-10.3.0/include -I/eb/maint/software/libpsl/0.21.1-GCCcore-10.3.0/include -I/eb/maint/software/GLib/2.68.2-GCCcore-10.3.0/include -I/eb/maint/software/SQLite/3.35.4-GCCcore-10.3.0/include -I/eb/maint/software/libxml2/2.9.10-GCCcore-10.3.0/include -I/eb/maint/software/GObject-Introspection/1.68.0-GCCcore-10.3.0/include -I/eb/maint/software/binutils/2.36.1-GCCcore-10.3.0/include -I/dev/shm/LibSoup/2.74.0/GCCcore-10.3.0/easybuild_obj -fvisibility=hidden -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -std=c99 -g -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -Wcast-align -Wdeclaration-after-statement -Wformat-nonliteral -Wformat-security -Wmissing-include-dirs -Wnested-externs -Wno-missing-field-initializers -Wno-sign-compare -Wno-unused-parameter -Wno-cast-function-type -Wpointer-arith -Wredundant-decls -Wswitch-default -Wswitch-enum -Wuninitialized -Werror=format-security -Werror=format=2 -Werror=empty-body -Werror=implicit-function-declaration -Werror=incompatible-pointer-types -Werror=pointer-arith -Werror=init-self -Werror=int-conversion -Werror=misleading-indentation -Werror=missing-include-dirs -Werror=overflow -Werror=return-type -Werror=shadow -Werror=strict-prototypes -Werror=undef -fstack-protector-strong -O2 -ftree-vectorize -march=native -fno-math-errno -std=gnu11 -fPIC -pthread -DSYSPROF_CAPTURE_COMPILATION -MD -MQ subprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p/sysprof-capture-writer-cat.c.o -MF subprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p/sysprof-capture-writer-cat.c.o.d -o subprojects/sysprof/src/libsysprof-capture/libsysprof-capture-4.a.p/sysprof-capture-writer-cat.c.o -c ../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-writer-cat.c
../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-writer-cat.c: In function translate_table_add:
../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-writer-cat.c:136:26: error: implicit declaration of function reallocarray [-Werror=implicit-function-declaration]
  136 |       table_ptr->items = reallocarray (table_ptr->items, table_ptr->n_items_allocated, sizeof (*table_ptr->items));
      |                          ^~~~~~~~~~~~
../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-writer-cat.c:136:26: warning: nested extern declaration of reallocarray [-Wnested-externs]
../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-writer-cat.c:136:24: error: assignment to TranslateItem * from i
nt makes pointer from integer without a cast [-Werror=int-conversion]
  136 |       table_ptr->items = reallocarray (table_ptr->items, table_ptr->n_items_allocated, sizeof (*table_ptr->items));
      |                        ^
../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-writer-cat.c: In function sysprof_capture_writer_cat:
../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-writer-cat.c:484:35: error: assignment to unsigned int * from in
t makes pointer from integer without a cast [-Werror=int-conversion]
  484 |                               ids = reallocarray (ids, n_elements_allocated, sizeof (*ids));
      |                                   ^
../libsoup-2.74.0/subprojects/sysprof/src/libsysprof-capture/sysprof-capture-writer-cat.c:485:38: error: assignment to SysprofCaptureCounterV
alue * from int makes pointer from integer without a cast [-Werror=int-conversion]
  485 |                               values = reallocarray (values, n_elements_allocated, sizeof (*values));
      |                                      ^
cc1: some warnings being treated as errors

Do I perhaps need to rebuild some components to fix these errors?

[akesandgren]

Closing this since foss/2021a is deprecated, see https://docs.easybuild.io/policies/toolchains

Sorry for not getting back to this @boegel

If this is still relevant, please consider opening a new pull request using a more recent toolchain