The gcc version is 8.3.0, git version is 2.34.1.
Fetching submodule 'utility'
- Submodule 'src/utility' (https://github.com/marbl/meryl-utility) registered for path 'utility'
- Cloning into '/home/hcaoad/Software/meryl/src/utility'...
- Submodule path 'utility': checked out '159a2d48eca5f208ed4473cc0139a5242f6ebbe3'
Building snapshot v1.4-development +61 changes (r1001 a2e291954d452f3e1b2772cf35a902181b32b4b4) (sync'd with github)
with utility v1.0-244-g159a2d4 159a2d48eca5f208ed4473cc0139a5242f6ebbe3
For 'Linux' '3.10.0-1062.el7.x86_64)' as 'amd64' into '/home/hcaoad/Software/meryl/build/{bin,obj}'.
Using GNU '/opt/ohpc/pub/compiler/gcc/8.3.0/bin/g++' version '8.3.0'.
g++ -o /home/hcaoad/Software/meryl/build/obj/lib/libmeryl.a/utility/src/align/align-ksw2-driver.o -c -MD -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DLIBBACKTRACE -mxsave -Wall -Wextra -Wformat -Wno-char-subscripts -Wno-sign-compare -Wno-unused-function -Wno-unused-parameter -Wno-unused-variable -Wno-deprecated-declarations -Wno-format-truncation -std=c++2a -pthread -fopenmp -fPIC -iquote/home/hcaoad/Software/meryl/src -iquotemeryl -iquoteutility/src utility/src/align/align-ksw2-driver.C
In file included from utility/src/system.H:26,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/system/time-v1.H:29:22: error: namespace name required before ‘inline’
namespace merylutil::inline system::inline v1 {
^~~~~~
utility/src/system/time-v1.H:29:22: error: expected ‘{’ before ‘inline’
utility/src/system/time-v1.H:29:29: error: ‘system’ does not name a type
namespace merylutil::inline system::inline v1 {
^~~~~~
In file included from utility/src/strings.H:23,
from utility/src/system/cpuIdent-v1.H:24,
from utility/src/system.H:28,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/datastructures/strings-v1.H:28:22: error: namespace name required before ‘inline’
namespace merylutil::inline strings::inline v1 {
^~~~~~
utility/src/datastructures/strings-v1.H:28:22: error: expected ‘{’ before ‘inline’
utility/src/datastructures/strings-v1.H:28:29: error: ‘strings’ does not name a type; did you mean ‘sprintf’?
namespace merylutil::inline strings::inline v1 {
^~~~~~~
sprintf
In file included from utility/src/strings.H:25,
from utility/src/system/cpuIdent-v1.H:24,
from utility/src/system.H:28,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/datastructures/keyAndValue-v1.H:25:22: error: namespace name required before ‘inline’
namespace merylutil::inline strings::inline v1 {
^~~~~~
utility/src/datastructures/keyAndValue-v1.H:25:22: error: expected ‘{’ before ‘inline’
utility/src/datastructures/keyAndValue-v1.H:25:29: error: ‘strings’ does not name a type; did you mean ‘sprintf’?
namespace merylutil::inline strings::inline v1 {
^~~~~~~
sprintf
In file included from utility/src/strings.H:26,
from utility/src/system/cpuIdent-v1.H:24,
from utility/src/system.H:28,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/datastructures/splitToWords-v1.H:28:22: error: namespace name required before ‘inline’
namespace merylutil::inline strings::inline v1 {
^~~~~~
utility/src/datastructures/splitToWords-v1.H:28:22: error: expected ‘{’ before ‘inline’
utility/src/datastructures/splitToWords-v1.H:28:29: error: ‘strings’ does not name a type; did you mean ‘sprintf’?
namespace merylutil::inline strings::inline v1 {
^~~~~~~
sprintf
In file included from utility/src/strings.H:27,
from utility/src/system/cpuIdent-v1.H:24,
from utility/src/system.H:28,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/datastructures/stringList-v1.H:35:22: error: namespace name required before ‘inline’
namespace merylutil::inline strings::inline v1 {
^~~~~~
utility/src/datastructures/stringList-v1.H:35:22: error: expected ‘{’ before ‘inline’
utility/src/datastructures/stringList-v1.H:35:29: error: ‘strings’ does not name a type; did you mean ‘sprintf’?
namespace merylutil::inline strings::inline v1 {
^~~~~~~
sprintf
In file included from utility/src/system.H:28,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/system/cpuIdent-v1.H:26:22: error: namespace name required before ‘inline’
namespace merylutil::inline system::inline v1 {
^~~~~~
utility/src/system/cpuIdent-v1.H:26:22: error: expected ‘{’ before ‘inline’
utility/src/system/cpuIdent-v1.H:26:29: error: ‘system’ does not name a type
namespace merylutil::inline system::inline v1 {
^~~~~~
In file included from utility/src/files.H:28,
from utility/src/system/logging-v1.H:24,
from utility/src/system.H:30,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/files/accessing-v1.H:34:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/accessing-v1.H:34:22: error: expected ‘{’ before ‘inline’
utility/src/files/accessing-v1.H:34:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
In file included from utility/src/files.H:29,
from utility/src/system/logging-v1.H:24,
from utility/src/system.H:30,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/files/reading-v1.H:45:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::v0 {
^~~~~~
utility/src/files/reading-v1.H:45:22: error: expected ‘{’ before ‘inline’
utility/src/files/reading-v1.H:45:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::v0 {
^~~~~
fileno
utility/src/files/reading-v1.H:50:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/reading-v1.H:50:22: error: expected ‘{’ before ‘inline’
utility/src/files/reading-v1.H:50:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
utility/src/files/reading-v1.H:78:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/reading-v1.H:78:22: error: expected ‘{’ before ‘inline’
utility/src/files/reading-v1.H:78:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
utility/src/files/reading-v1.H:116:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/reading-v1.H:116:22: error: expected ‘{’ before ‘inline’
utility/src/files/reading-v1.H:116:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
In file included from utility/src/files.H:30,
from utility/src/system/logging-v1.H:24,
from utility/src/system.H:30,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/files/writing-v1.H:48:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/writing-v1.H:48:22: error: expected ‘{’ before ‘inline’
utility/src/files/writing-v1.H:48:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
utility/src/files/writing-v1.H:85:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/writing-v1.H:85:22: error: expected ‘{’ before ‘inline’
utility/src/files/writing-v1.H:85:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
In file included from utility/src/files.H:32,
from utility/src/system/logging-v1.H:24,
from utility/src/system.H:30,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/files/buffered-v1-reading.H:29:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/buffered-v1-reading.H:29:22: error: expected ‘{’ before ‘inline’
utility/src/files/buffered-v1-reading.H:29:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
In file included from utility/src/files.H:33,
from utility/src/system/logging-v1.H:24,
from utility/src/system.H:30,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/files/buffered-v1-writing.H:25:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/buffered-v1-writing.H:25:22: error: expected ‘{’ before ‘inline’
utility/src/files/buffered-v1-writing.H:25:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
In file included from utility/src/files.H:35,
from utility/src/system/logging-v1.H:24,
from utility/src/system.H:30,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/files/compressed-v1.H:25:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/compressed-v1.H:25:22: error: expected ‘{’ before ‘inline’
utility/src/files/compressed-v1.H:25:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
In file included from utility/src/files.H:36,
from utility/src/system/logging-v1.H:24,
from utility/src/system.H:30,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/files/compressed-v1-reading.H:26:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/compressed-v1-reading.H:26:22: error: expected ‘{’ before ‘inline’
utility/src/files/compressed-v1-reading.H:26:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
In file included from utility/src/files.H:37,
from utility/src/system/logging-v1.H:24,
from utility/src/system.H:30,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/files/compressed-v1-writing.H:26:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/compressed-v1-writing.H:26:22: error: expected ‘{’ before ‘inline’
utility/src/files/compressed-v1-writing.H:26:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
In file included from utility/src/files.H:39,
from utility/src/system/logging-v1.H:24,
from utility/src/system.H:30,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/files/memoryMapped-v1.H:48:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/memoryMapped-v1.H:48:22: error: expected ‘{’ before ‘inline’
utility/src/files/memoryMapped-v1.H:48:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
In file included from utility/src/files.H:41,
from utility/src/system/logging-v1.H:24,
from utility/src/system.H:30,
from utility/src/align/align-ksw2-driver.H:20,
from utility/src/align/align-ksw2-driver.C:20:
utility/src/files/fasta-fastq-v1.H:23:22: error: namespace name required before ‘inline’
namespace merylutil::inline files::inline v1 {
^~~~~~
utility/src/files/fasta-fastq-v1.H:23:22: error: expected ‘{’ before ‘inline’
utility/src/files/fasta-fastq-v1.H:23:29: error: ‘files’ does not name a type; did you mean ‘fileno’?
namespace merylutil::inline files::inline v1 {
^~~~~
fileno
In file included from utility/src/align/align-ksw2-driver.C:20:
utility/src/align/align-ksw2-driver.H:25:22: error: namespace name required before ‘inline’
namespace merylutil::inline align::inline ksw2::inline v1 {
^~~~~~
utility/src/align/align-ksw2-driver.H:25:22: error: expected ‘{’ before ‘inline’
utility/src/align/align-ksw2-driver.H:25:29: error: ‘align’ does not name a type; did you mean ‘asin’?
namespace merylutil::inline align::inline ksw2::inline v1 {
^~~~~
asin
In file included from utility/src/align/align-ksw2-driver.C:21:
utility/src/align/align-ksw2.H:16:22: error: namespace name required before ‘inline’
namespace merylutil::inline align::inline ksw2::inline v1 {
^~~~~~
utility/src/align/align-ksw2.H:16:22: error: expected ‘{’ before ‘inline’
utility/src/align/align-ksw2.H:16:29: error: ‘align’ does not name a type; did you mean ‘asin’?
namespace merylutil::inline align::inline ksw2::inline v1 {
^~~~~
asin
In file included from utility/src/arrays.H:23,
from utility/src/align/align-ksw2-driver.C:23:
utility/src/datastructures/arrays-v1.H:25:22: error: namespace name required before ‘inline’
namespace merylutil::inline arrays::inline v1 {
^~~~~~
utility/src/datastructures/arrays-v1.H:25:22: error: expected ‘{’ before ‘inline’
utility/src/datastructures/arrays-v1.H:25:29: error: ‘arrays’ does not name a type
namespace merylutil::inline arrays::inline v1 {
^~~~~~
In file included from utility/src/sequence.H:23,
from utility/src/align/align-ksw2-driver.C:25:
utility/src/sequence/sequence-v1.H:26:22: error: namespace name required before ‘inline’
namespace merylutil::inline sequence::inline v1 {
^~~~~~
utility/src/sequence/sequence-v1.H:26:22: error: expected ‘{’ before ‘inline’
utility/src/sequence/sequence-v1.H:26:29: error: ‘sequence’ does not name a type; did you mean ‘sigqueue’?
namespace merylutil::inline sequence::inline v1 {
^~~~~~~~
sigqueue
In file included from utility/src/sequence.H:25,
from utility/src/align/align-ksw2-driver.C:25:
utility/src/sequence/dnaSeq-v1.H:47:22: error: namespace name required before ‘inline’
namespace merylutil::inline sequence::inline v1 {
^~~~~~
utility/src/sequence/dnaSeq-v1.H:47:22: error: expected ‘{’ before ‘inline’
utility/src/sequence/dnaSeq-v1.H:47:29: error: ‘sequence’ does not name a type; did you mean ‘sigqueue’?
namespace merylutil::inline sequence::inline v1 {
^~~~~~~~
sigqueue
In file included from utility/src/sequence.H:26,
from utility/src/align/align-ksw2-driver.C:25:
utility/src/sequence/dnaSeqFile-v1.H:70:22: error: namespace name required before ‘inline’
namespace merylutil::inline sequence::inline v1 {
^~~~~~
utility/src/sequence/dnaSeqFile-v1.H:70:22: error: expected ‘{’ before ‘inline’
utility/src/sequence/dnaSeqFile-v1.H:70:29: error: ‘sequence’ does not name a type; did you mean ‘sigqueue’?
namespace merylutil::inline sequence::inline v1 {
^~~~~~~~
sigqueue
utility/src/align/align-ksw2-driver.C:27:22: error: namespace name required before ‘inline’
namespace merylutil::inline align::inline ksw2::inline v1 {
^~~~~~
utility/src/align/align-ksw2-driver.C:27:22: error: expected ‘{’ before ‘inline’
utility/src/align/align-ksw2-driver.C:27:29: error: ‘align’ does not name a type; did you mean ‘asin’?
namespace merylutil::inline align::inline ksw2::inline v1 {
^~~~~
asin
make: *** [/home/hcaoad/Software/meryl/build/obj/lib/libmeryl.a/utility/src/align/align-ksw2-driver.o] Error 1