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marbl / meryl

A genomic k-mer counter (and sequence utility) with nice features.
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Compile error #38

Closed Han-Cao closed 1 year ago

Han-Cao commented 1 year ago

Hi,

I have the same error in #37. I tried to fix this by compiling from source. However, I have the below error when compiling.

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
brianwalenz commented 1 year ago

Unfortunately, this is caused by a "recent" fix in the C++ standard that gcc-8 does not support - "recent", as in late 2018; https://www.open-std.org/jtc1/sc22/wg21/docs/papers/2018/p1094r2.html.

gcc-8.3 is extremely out of date (February 2019); the most mature supported version of gcc is 11.4.

Han-Cao commented 1 year ago

Hi @brianwalenz

As README said dependency is gcc 7.4.0 or higher, I thought gcc-8.3 was fine to use. After using the latest gcc, there is no error now.

Thanks a lot.