[package - main-arm64-default][biology/ncbi-toolkit] Failed for ncbi-toolkit-2017.01.06_6 in stage
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue Apr 20 19:47:12 UTC 2021
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 at FreeBSD.org
Last committer: @FreeBSD.org
Ident: Makefile ident:
Log URL: http://ampere2.nyi.freebsd.org/data/main-arm64-default/p338d8ba0f777_s5a89498d19/logs/ncbi-toolkit-2017.01.06_6.log
Build URL: http://ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=p338d8ba0f777_s5a89498d19
Log:
=>> Building biology/ncbi-toolkit
build started at Tue Apr 20 19:29:27 UTC 2021
port directory: /usr/ports/biology/ncbi-toolkit
package name: ncbi-toolkit-2017.01.06_6
building for: FreeBSD main-arm64-default-job-05 14.0-CURRENT FreeBSD 14.0-CURRENT 1400008 arm64
maintained by: yuri at FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-8-gaf08dbda
Host OSVERSION: 1300139
Jail OSVERSION: 1400008
Job Id: 05
!!! Jail is newer than host. (Jail: 1400008, Host: 1300139) !!!
!!! 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_6:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri at FreeBSD.org
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--CONFIGURE_ARGS--
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=======================<phase: check-sanity >============================
===========================================================================
=======================<phase: pkg-depends >============================
===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.16.3.txz
[main-arm64-default-job-05] Installing pkg-1.16.3...
[main-arm64-default-job-05] Extracting pkg-1.16.3: .......... done
===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of ncbi-toolkit-2017.01.06_6
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_6 for building
===========================================================================
=======================<phase: checksum >============================
===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_6 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_6 for building
===> Extracting for ncbi-toolkit-2017.01.06_6
=> SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for ncbi-toolkit-2017.01.06_6
===> Applying FreeBSD patches for ncbi-toolkit-2017.01.06_6 from /usr/ports/biology/ncbi-toolkit/files
===========================================================================
=======================<phase: build-depends >============================
===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found
===> Installing existing package /packages/All/libX11-1.6.12,1.txz
[main-arm64-default-job-05] Installing libX11-1.6.12,1...
[main-arm64-default-job-05] `-- Installing libxcb-1.14_1...
[main-arm64-default-job-05] | `-- Installing libXau-1.0.9...
[main-arm64-default-job-05] | `-- Extracting libXau-1.0.9: .......... done
[main-arm64-default-job-05] | `-- Installing libXdmcp-1.1.3...
[main-arm64-default-job-05] | | `-- Installing xorgproto-2020.1...
[main-arm64-default-job-05] | | `-- Extracting xorgproto-2020.1: .......... done
[main-arm64-default-job-05] | `-- Extracting libXdmcp-1.1.3: ......... done
<snip>
sequin1.c:20931:13: warning: enumeration value 'eVirusClass_Unknown' not handled in switch [-Wswitch]
switch (wiz->virus_class) {
^
sequin1.c:21036:13: warning: enumeration value 'eCulturedKingdom_Unknown' not handled in switch [-Wswitch]
switch (wiz->cultured_kingdom) {
^
sequin1.c:21347:11: warning: enumeration value 'eWizardType_NormalDialogs' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^
sequin1.c:21394:10: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
-Use the <93>Import Source Table<94> button to import a tab-delimited table\n\
^~~~ ~~~~
sequin1.c:21552:10: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
-Use the <93>Import Source Table<94> button to import a tab-delimited table\n\
^~~~ ~~~~
sequin1.c:21632:10: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
-Use the <93>Import Source Table<94> button to import a tab-delimited table\n\
^~~~ ~~~~
sequin1.c:22401:11: warning: enumeration values 'eWizardType_NormalDialogs' and 'eWizardType_WGS' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^
sequin1.c:27538:11: warning: enumeration values 'eWizardType_NormalDialogs', 'eWizardType_Microsatellite', and 'eWizardType_WGS' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^
sequin1.c:28943:13: warning: 4 enumeration values not handled in switch: 'eWizardType_NormalDialogs', 'eWizardType_Microsatellite', 'eWizardType_DLoop'... [-Wswitch]
switch (wiz->wizard_type) {
^
sequin1.c:28976:11: warning: 5 enumeration values not handled in switch: 'eWizardType_NormalDialogs', 'eWizardType_UnculturedSamples', 'eWizardType_Microsatellite'... [-Wswitch]
switch (wiz->wizard_type) {
^
sequin1.c:29038:11: warning: 5 enumeration values not handled in switch: 'eWizardType_NormalDialogs', 'eWizardType_UnculturedSamples', 'eWizardType_Microsatellite'... [-Wswitch]
switch (wiz->wizard_type) {
^
sequin1.c:32916:58: warning: data argument not used by format string [-Wformat-extra-args]
fprintf (lip->fp, "%s (too short)\n", a->id, "Low Quality");
~~~~~~~~~~~~~~~~~~ ^
sequin1.c:33416:7: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
Click <91>Import Nucleotide Alignment<92> to load your nucleotide alignment file.\n\
^~~~ ~~~~
sequin1.c:33417:7: warning: illegal character encoding in string literal [-Winvalid-source-encoding]
Click <91>Custom Alignment Settings<92> if there is trouble reading your alignment file.\n\
^~~~ ~~~~
sequin1.c:33916:11: warning: 7 enumeration values not handled in switch: 'eWizardType_NormalDialogs', 'eWizardType_UnculturedSamples', 'eWizardType_Viruses'... [-Wswitch]
switch (frm->wiz->wizard_type) {
^
sequin1.c:34038:11: warning: enumeration values 'eWizardType_NormalDialogs' and 'eWizardType_WGS' not handled in switch [-Wswitch]
switch (frm->wiz->wizard_type) {
^
sequin1.c:34089:11: warning: enumeration values 'eWizardType_NormalDialogs' and 'eWizardType_WGS' not handled in switch [-Wswitch]
switch (wiz->wizard_type) {
^
26 warnings generated.
sequin2.c:7795:56: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion]
if (sep == NULL || StringHasNoText (valname)) return FALSE;
^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
sequin2.c:7796:33: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion]
if (! IS_Bioseq (sep)) return FALSE;
^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
sequin2.c:7798:68: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion]
if (bsp == NULL || bsp->mol != mol || bsp->descr == NULL) return FALSE;
^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
sequin2.c:7800:57: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_CharPtr' (aka 'char *') [-Wnon-literal-null-conversion]
if (vnp == NULL || vnp->data.ptrvalue == NULL) return FALSE;
^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
sequin2.c:27333:57: warning: expression which evaluates to zero treated as a null pointer constant of type 'BioseqPtr' (aka 'struct bioseq *') [-Wnon-literal-null-conversion]
if (sep == NULL || sep->data.ptrvalue == NULL) return FALSE;
^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
sequin2.c:27348:32: warning: expression which evaluates to zero treated as a null pointer constant of type 'BioseqPtr' (aka 'struct bioseq *') [-Wnon-literal-null-conversion]
if (!IS_Bioseq (sep)) return FALSE;
^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
6 warnings generated.
sequin4.c:4989:52: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion]
salp = Sequin_GlobalAlign2Seq(bsp, sbp->bsp, FALSE);
^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
sequin4.c:4993:49: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion]
salp = Sqn_GlobalAlign2Seq(bsp, sbp->bsp, FALSE);
^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
sequin4.c:14072:67: warning: expression which evaluates to zero treated as a null pointer constant of type 'Nlm_BoolPtr' (aka 'unsigned char *') [-Wnon-literal-null-conversion]
salp = Sequin_GlobalAlign2Seq(master_bsp, vnp->data.ptrvalue, FALSE);
^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
3 warnings generated.
sequin5.c:18184:12: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion]
return FALSE;
^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
sequin5.c:19773:12: warning: expression which evaluates to zero treated as a null pointer constant of type 'ValNodePtr' (aka 'struct valnode *') [-Wnon-literal-null-conversion]
return FALSE;
^~~~~
./include/ncbistd.h:247:15: note: expanded from macro 'FALSE'
#define FALSE ((Nlm_Boolean)0)
^~~~~~~~~~~~~~~~
2 warnings generated.
sequin6.c:11491:12: warning: comparison of array 'hfp->file' equal to a null pointer is always false [-Wtautological-pointer-compare]
if (hfp->file == NULL || hfp->file [0] == '\0') return FALSE;
~~~~~^~~~ ~~~~
sequin6.c:11766:12: warning: comparison of array 'hfp->file' equal to a null pointer is always false [-Wtautological-pointer-compare]
if (hfp->file == NULL || hfp->file [0] == '\0') return FALSE;
~~~~~^~~~ ~~~~
2 warnings generated.
sequin8.c:10165:39: warning: self-comparison always evaluates to true [-Wtautological-compare]
} else if (left2 <= left1 && right2 >= right2) {
^
sequin8.c:10507:69: warning: self-comparison always evaluates to false [-Wtautological-compare]
if (tpa_conflict != eIntervalConflict_none || prim_conflict != prim_conflict) {
^
sequin8.c:10513:69: warning: self-comparison always evaluates to false [-Wtautological-compare]
if (tpa_conflict != eIntervalConflict_none || prim_conflict != prim_conflict) {
^
sequin8.c:17767:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
} else if (fcontext2.itemID < fcontext2.itemID) {
^
4 warnings generated.
sequin9.c:2710:7: warning: comparison of array 'path' equal to a null pointer is always false [-Wtautological-pointer-compare]
if (path == NULL || config == NULL || config->data.ptrvalue == NULL) return;
^~~~ ~~~~
1 warning generated.
: Psequin
cc -o sbtedit -I. -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF -UINTERNAL_NCBI_SEQUIN sbtedit.c -lncbicn3d -lddvlib -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb -lncbitxc2 -lncbiid1 -lnetblast -lncbitool -lblastcompadj -lncbimla -lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbiobj -lncbi -L/usr/local/lib -lXm -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm
: sbtedit
cc -o Nentrez -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF entrez.c -lncbiid1 -lvibnet -lncbicn3d -lncbidesk -lblastapi -lblast -lncbimmdb -lddvlib -lnetblast -lncbitool -lblastcompadj -lncbiNacc -lnetentr -lnetcli -lncbiacc -lvibrant -lncbicdr -lncbiobj -lncbi -L/usr/local/lib -lXm -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm
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 -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" udvmain.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
cc -o udv -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF udvmain.o -lncbiid1 -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb -lddvlib -lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbitool -lblastcompadj -lncbiobj -lncbi -L/usr/local/lib -lXm -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm
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 -DNETENTREZVERSION="\"2.02c2ASN1SPEC6 \"" ddvmain.c
cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument]
ddvmain.c:147:13: warning: 'extern' variable has an initializer [-Wextern-initializer]
extern Args DDV_myargs[NUMARGS] = {
^
1 warning generated.
cc -o ddv -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF ddvmain.o -lncbiid1 -lvibnet -lncbidesk -lblastapi -lblast -lncbimmdb -lddvlib -lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbitool -lblastcompadj -lncbiobj -lncbi -L/usr/local/lib -lXm -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm
cc -g -o blastcl3 -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF -DBLAST_CS_API blastall.c -lblastapi -lblast -lnetblast -lncbitool -lblastcompadj -lnetcli -lncbiobj -lncbi -lm
cc -g -o idfetch -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF idfetch.c -lncbiid1 -lnetcli -lncbiobj -lconnssl -lncbi -lm
idfetch.c:1422:38: warning: format specifies type 'short' but the argument has type 'Nlm_Int4' (aka 'int') [-Wformat]
sprintf( pFormat, "%%s%%0%hdhd", DigitsStart);
~~~ ^~~~~~~~~~~
%d
1 warning generated.
cc -g -o asn2gb -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF asn2gb.c -lncbiid1 -lnetcli -lncbitool -lblastcompadj -lncbiobj -lconnssl -lncbi -lm
cc -o tbl2asn -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF tbl2asn.c -lncbitool -lblastcompadj -lncbiobj -lnetcli -lconnssl -lncbi -lm
cc -g -o gene2xml -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF gene2xml.c -lnetcli -lncbiobj -lncbi -lm
cc -g -o entrez2 -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF entrez2.c -lncbiid1 -lnetcli -lncbidesk -lblastapi -lblast -lncbimmdb -lncbitool -lblastcompadj -lncbiobj -lvibrant -lncbi -L/usr/local/lib -lXm -lXpm -lXft -lfontconfig -lXrender -ljpeg -lpng -lz -lXmu -lXau -lXt -lX11 -lXext -lm
: entrez2
cc -g -o gbseqget -O -I../include -L../lib -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF gbseqget.c -lncbiid1 -lnetcli -lncbitool -lblastcompadj -lncbiobj -lncbi -lm
Put the date stamp to the file ../VERSION
*********************************************************
*The new binaries are located in ./ncbi/build/ directory*
*********************************************************
===========================================================================
=======================<phase: run-depends >============================
===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found
===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xau.pc - found
===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found
===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xft.pc - found
===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found
===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xrender.pc - found
===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found
===> ncbi-toolkit-2017.01.06_6 depends on file: /usr/local/libdata/pkgconfig/xpm.pc - found
===========================================================================
=======================<phase: stage >============================
===> Staging for ncbi-toolkit-2017.01.06_6
===> Generating temporary packing list
cd /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/bin && install -s -m 555 * /wrkdirs/usr/ports/biology/ncbi-toolkit/work/stage/usr/local/bin
cd /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/lib && install -m 0644 *.a /wrkdirs/usr/ports/biology/ncbi-toolkit/work/stage/usr/local/lib/ncbi
cd /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/include && install -m 0644 *.h /wrkdirs/usr/ports/biology/ncbi-toolkit/work/stage/usr/local/include/ncbi
cd /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/include/connect && install -m 0644 *.h /wrkdirs/usr/ports/biology/ncbi-toolkit/work/stage/usr/local/include/ncbi/connect
cd /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/doc/man && install -m 444 * /wrkdirs/usr/ports/biology/ncbi-toolkit/work/stage/usr/local/man/man1
cd /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/data && install -m 0644 * /wrkdirs/usr/ports/biology/ncbi-toolkit/work/stage/usr/local/share/ncbi-toolkit
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/ncbi-toolkit
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