[package - main-amd64-default][biology/ncbi-toolkit] Failed for ncbi-toolkit-2017.01.06_7 in build
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Date: Wed, 07 Jun 2023 11:59:26 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/beefy18/data/main-amd64-default/p24b08fa76284_sd66540e829/logs/ncbi-toolkit-2017.01.06_7.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p24b08fa76284_sd66540e829
Log:
=>> Building biology/ncbi-toolkit
build started at Wed Jun 7 11:57:09 UTC 2023
port directory: /usr/ports/biology/ncbi-toolkit
package name: ncbi-toolkit-2017.01.06_7
building for: FreeBSD main-amd64-default-job-11 14.0-CURRENT FreeBSD 14.0-CURRENT 1400089 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1400089
Job Id: 11
!!! Jail is newer than host. (Jail: 1400089, Host: 1400073) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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===> The following configuration options are available for ncbi-toolkit-2017.01.06_7:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
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--CONFIGURE_ARGS--
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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-amd64-default-job-11] Installing pkg-1.19.1_1...
[main-amd64-default-job-11] 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-amd64-default-job-11] Installing libX11-1.7.2,1...
[main-amd64-default-job-11] `-- Installing libxcb-1.15_1...
[main-amd64-default-job-11] | `-- Installing libXau-1.0.9...
<snip>
sprintf (cip->description, fmt);
^~~
sqnutil3.c:33201:35: note: treat the string as an argument to avoid this
sprintf (cip->description, fmt);
^
"%s",
sqnutil3.c:34051:38: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion]
if (StringHasNoText (name)) return FALSE;
^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
4 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 sqnutil4.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
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: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:28869:17: 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: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)) {
~~~~~ ^ ~~~
7 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