[package - main-arm64-default][biology/ncbi-toolkit] Failed for ncbi-toolkit-2017.01.06_7 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Wed, 29 Mar 2023 16:24:32 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.

Maintainer:     yuri@FreeBSD.org
Log URL:        https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/pd55ec1db8ffa_s9b20ab1e1e/logs/ncbi-toolkit-2017.01.06_7.log
Build URL:      https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=pd55ec1db8ffa_s9b20ab1e1e
Log:

=>> Building biology/ncbi-toolkit
build started at Wed Mar 29 16:19:12 UTC 2023
port directory: /usr/ports/biology/ncbi-toolkit
package name: ncbi-toolkit-2017.01.06_7
building for: FreeBSD main-arm64-default-job-07 14.0-CURRENT FreeBSD 14.0-CURRENT 1400084 arm64
maintained by: yuri@FreeBSD.org
Makefile ident: 
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1400084
Job Id: 07




!!! Jail is newer than host. (Jail: 1400084, Host: 1400073) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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=======================<phase: check-sanity   >============================
===========================================================================
=======================<phase: pkg-depends    >============================
===>   ncbi-toolkit-2017.01.06_7 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-arm64-default-job-07] Installing pkg-1.19.1_1...
[main-arm64-default-job-07] Extracting pkg-1.19.1_1: .......... done
===>   ncbi-toolkit-2017.01.06_7 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of ncbi-toolkit-2017.01.06_7
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_7 for building
===========================================================================
=======================<phase: checksum       >============================
===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_7 for building
=> SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_7 for building
===>  Extracting for ncbi-toolkit-2017.01.06_7
=> SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for ncbi-toolkit-2017.01.06_7
===>  Applying FreeBSD patches for ncbi-toolkit-2017.01.06_7 from /usr/ports/biology/ncbi-toolkit/files
===========================================================================
=======================<phase: build-depends  >============================
===>   ncbi-toolkit-2017.01.06_7 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found
===>   Installing existing package /packages/All/libX11-1.7.2,1.pkg
[main-arm64-default-job-07] Installing libX11-1.7.2,1...
[main-arm64-default-job-07] `-- Installing libxcb-1.15_1...
[main-arm64-default-job-07] |   `-- Installing libXau-1.0.9...
[main-arm64-default-job-07] |   `-- Extracting libXau-1.0.9: .......... done
<snip>
sqnutil4.c:7308:53: warning: expression which evaluates to zero treated as a null pointer constant of type 'DeflineFeatureRequestListPtr' (aka 'struct deflinefeaturerequestlist *') [-Wnon-literal-null-conversion]
  expected_product_name = GetProductName (cds, bsp, FALSE);
                                                    ^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
              ^~~~~~~~~~~~~~~~
sqnutil4.c:10750:37: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion]
        if (new_fcp == NULL) return FALSE;
                                    ^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
              ^~~~~~~~~~~~~~~~
sqnutil4.c:10752:33: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion]
        if (vnp == NULL) return FALSE;
                                ^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
              ^~~~~~~~~~~~~~~~
sqnutil4.c:20501:34: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
  while (line != NULL && line[0] != EOF) {
                         ~~~~~~~ ^  ~~~
sqnutil4.c:20579:34: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
  while (line != NULL && line[0] != EOF) {
                         ~~~~~~~ ^  ~~~
sqnutil4.c:27751:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion]
  if (sdp == NULL) return FALSE;
                          ^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
              ^~~~~~~~~~~~~~~~
sqnutil4.c:27753:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion]
  if (pdp == NULL) return FALSE;
                          ^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
              ^~~~~~~~~~~~~~~~
sqnutil4.c:28869:32: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
    while (*val <= 256 && *val >= -1 && isspace (*val)) {
                          ~~~~ ^  ~~
sqnutil4.c:28869:17: warning: result of comparison of constant 256 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
    while (*val <= 256 && *val >= -1 && isspace (*val)) {
           ~~~~ ^  ~~~
sqnutil4.c:28920:34: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
  while (line != NULL && line[0] != EOF) {
                         ~~~~~~~ ^  ~~~
sqnutil4.c:28931:50: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
      while (last > val && *last <= 256 && *last >= -1 && isspace (*last)) {
                                           ~~~~~ ^  ~~
sqnutil4.c:28931:34: warning: result of comparison of constant 256 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
      while (last > val && *last <= 256 && *last >= -1 && isspace (*last)) {
                           ~~~~~ ^  ~~~
12 warnings generated.
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c  -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF subutil.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
subutil.c:774:41: warning: expression which evaluates to zero treated as a null pointer constant of type 'SeqLitPtr' (aka 'struct seqlit *') [-Wnon-literal-null-conversion]
    if (delta_seq_entry == NULL) return FALSE;
                                        ^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
              ^~~~~~~~~~~~~~~~
subutil.c:775:48: warning: expression which evaluates to zero treated as a null pointer constant of type 'SeqLitPtr' (aka 'struct seqlit *') [-Wnon-literal-null-conversion]
    if (IS_Bioseq_set(delta_seq_entry)) return FALSE;
                                               ^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
              ^~~~~~~~~~~~~~~~
subutil.c:776:56: warning: expression which evaluates to zero treated as a null pointer constant of type 'SeqLitPtr' (aka 'struct seqlit *') [-Wnon-literal-null-conversion]
    if (delta_seq_entry->data.ptrvalue == NULL) return FALSE;
                                                       ^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
              ^~~~~~~~~~~~~~~~
subutil.c:782:16: warning: expression which evaluates to zero treated as a null pointer constant of type 'SeqLitPtr' (aka 'struct seqlit *') [-Wnon-literal-null-conversion]
        return FALSE;
               ^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
              ^~~~~~~~~~~~~~~~
subutil.c:3639:32: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare]
            if (AA_for_tRNA != '\0')
                               ^~~~
                               (void *)0
subutil.c:4050:16: warning: expression which evaluates to zero treated as a null pointer constant of type 'SeqGraphPtr' (aka 'struct seqgraph *') [-Wnon-literal-null-conversion]
        return FALSE;
               ^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
              ^~~~~~~~~~~~~~~~
6 warnings generated.
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c  -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF edutil.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
edutil.c:2062:48: warning: expression which evaluates to zero treated as a null pointer constant of type 'BioseqPtr' (aka 'struct bioseq *') [-Wnon-literal-null-conversion]
    if ((oldbsp == NULL) || (from < 0)) return FALSE;
                                               ^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
              ^~~~~~~~~~~~~~~~
edutil.c:2203:50: warning: expression which evaluates to zero treated as a null pointer constant of type 'BioseqPtr' (aka 'struct bioseq *') [-Wnon-literal-null-conversion]
    if ((sourceid == NULL) || (from < 0)) return FALSE;
                                                 ^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
              ^~~~~~~~~~~~~~~~
2 warnings generated.
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c  -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF asn2ff1.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c  -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF asn2ff2.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
asn2ff2.c:1358:8: warning: type specifier missing, defaults to 'int'; ISO C99 and later do not support implicit int [-Wimplicit-int]
static ChoicePID(SeqIdPtr sid) 
~~~~~~ ^
int
1 warning generated.
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c  -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF asn2ff3.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
asn2ff3.c:2717:28: warning: format specifies type 'char *' but the argument has type 'Nlm_VoidPtr' (aka 'void *') [-Wformat]
        sprintf(val, "GeneID:%s", vnp->data.ptrvalue);
                             ~~   ^~~~~~~~~~~~~~~~~~
1 warning generated.
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c  -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF asn2ff4.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
asn2ff4.c:1126:5: warning: add explicit braces to avoid dangling else [-Wdangling-else]
                        }else{
                         ^
asn2ff4.c:1347:8: warning: type specifier missing, defaults to 'int'; ISO C99 and later do not support implicit int [-Wimplicit-int]
static CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2)
~~~~~~ ^
int
asn2ff4.c:2069:26: warning: comparison of array 'gbp->accession' equal to a null pointer is always false [-Wtautological-pointer-compare]
        if (gbp == NULL || gbp->accession == NULL)
                           ~~~~~^~~~~~~~~    ~~~~
asn2ff4.c:2660:12: warning: address of array 'gbp->locus' will always evaluate to 'true' [-Wpointer-bool-conversion]
                if (gbp->locus) {
                ~~  ~~~~~^~~~~
asn2ff4.c:2664:12: warning: address of array 'gbp->accession' will always evaluate to 'true' [-Wpointer-bool-conversion]
                if (gbp->accession) {
                ~~  ~~~~~^~~~~~~~~
5 warnings generated.
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c  -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF asn2ff5.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
asn2ff5.c:1683:5: warning: add explicit braces to avoid dangling else [-Wdangling-else]
                                else
                                ^
asn2ff5.c:2128:10: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion]
                temp = '\0';
                       ^~~~
asn2ff5.c:2124:12: warning: expression result unused [-Wunused-value]
                        temp++; *ptr_in++;
                                ^~~~~~~~~
3 warnings generated.
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c  -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF asn2ff6.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c  -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF asn2gnb1.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -c  -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF asn2gnb2.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
asn2gnb2.c:1742:18: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare]
  while (accp != '\0'  &&  prevp != '\0') {
                 ^~~~
                 (void *)0
asn2gnb2.c:1742:37: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare]
  while (accp != '\0'  &&  prevp != '\0') {
                                    ^~~~
                                    (void *)0
asn2gnb2.c:1767:41: warning: comparing a pointer to a null character constant; did you mean to compare to NULL? [-Wpointer-compare]
    for (ptr = acc, letters = 0; ptr != '\0'  &&  IS_ALPHA(*ptr); ++ptr, ++letters) continue;
                                        ^~~~
                                        (void *)0
asn2gnb2.c:3409:14: warning: call to undeclared function 'PrintDate'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
    string = PrintDate (spb->created);
             ^
asn2gnb2.c:3409:12: error: incompatible integer to pointer conversion assigning to 'Nlm_CharPtr' (aka 'char *') from 'int' [-Wint-conversion]
    string = PrintDate (spb->created);
           ^ ~~~~~~~~~~~~~~~~~~~~~~~~
asn2gnb2.c:3417:14: warning: call to undeclared function 'PrintDate'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
    string = PrintDate (spb->sequpd);
             ^
asn2gnb2.c:3417:12: error: incompatible integer to pointer conversion assigning to 'Nlm_CharPtr' (aka 'char *') from 'int' [-Wint-conversion]
    string = PrintDate (spb->sequpd);
           ^ ~~~~~~~~~~~~~~~~~~~~~~~
asn2gnb2.c:3424:14: warning: call to undeclared function 'PrintDate'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
    string = PrintDate (spb->annotupd);
             ^
asn2gnb2.c:3424:12: error: incompatible integer to pointer conversion assigning to 'Nlm_CharPtr' (aka 'char *') from 'int' [-Wint-conversion]
    string = PrintDate (spb->annotupd);
           ^ ~~~~~~~~~~~~~~~~~~~~~~~~~
6 warnings and 3 errors generated.
*** Error code 1

Stop.
make[1]: stopped in /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/build

Fatal error building NCBI core libraries.
Please be sure that you have X11 and Motif libraries installed.
The NCBI toolkit FAQ at ftp://ftp.ncbi.nih.gov/toolbox/FAQ.html may be helpful.

*** Error code 1

Stop.
make: stopped in /usr/ports/biology/ncbi-toolkit