"@" symbol in directory path results in syntax error in Config_heavy.pl

[ZRE-Services]

Description

Using a directory path with "@" in a Ubuntu system causes a syntax error. The "@" symbol is interpreted as a variable instead of a part of the directory name.

Steps to Reproduce

Set a directory path containing "@" and attempt to use it in a Perl script.
Example path: /home/bioinformatics@example.de/miniconda3/envs/bismark/lib/perl5/5.32/core_perl/Config_heavy.pl

Expected behavior
The path should be recognized correctly, and no syntax error should occur.

perl -V output goes here

Summary of my perl5 (revision 5 version 32 subversion 1) configuration:
   
  Platform:
    osname=linux
    osvers=6.2.0-1018-azure
    archname=x86_64-linux-thread-multi
    uname='linux a9829a0f1755 6.2.0-1018-azure #18~22.04.1-ubuntu smp tue nov 21 19:25:02 utc 2023 x86_64 x86_64 x86_64 gnulinux '
    config_args='-de -Dprefix=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark -Dvendorprefix=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark -Dscriptdir=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin -Dsitescript=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin -Dvendorscript=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin -Duserelocatableinc -Duseshrplib -Dinc_version_list=none -Dprivlib=.../../lib/perl5/core_perl -Dsitelib=.../../lib/perl5/site_perl -Dvendorlib=.../../lib/perl5/vendor_perl -Darchlib=.../../lib/perl5/5.32/core_perl -Dsitearch=.../../lib/perl5/5.32/site_perl -Dvendorarch=.../../lib/perl5/5.32/vendor_perl -Dinstallusrbinperl=n -Dusethreads -Dcccdlflags=-fPIC -Dldflags=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib -Wl,-rpath-link,/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib -L/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib  -Ddefault_inc_excludes_dot=n -Dccflags=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/perl_1703310062586/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark=/usr/local/src/conda-prefix -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -Dcc=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//bin/x86_64-conda-linux-gnu-gcc -Dar=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//bin/x86_64-conda-linux-gnu-ar -Dlddlflags=-shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib -Wl,-rpath-link,/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib -L/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib -Dsysroot=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//x86_64-conda-linux-gnu/sysroot -Dmyhostname=conda -Dmydomain=.conda -Dperladmin=conda -Dcf_by=conda -Dcf_email=conda -Dsysman=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/man/man1 -Dman1dir=.../../man/man1 -Dman3dir=.../../man/man3'
    hint=recommended
    useposix=true
    d_sigaction=define
    useithreads=define
    usemultiplicity=define
    use64bitint=define
    use64bitall=define
    uselongdouble=undef
    usemymalloc=n
    default_inc_excludes_dot=undef
    bincompat5005=undef
  Compiler:
    cc='/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//bin/x86_64-conda-linux-gnu-gcc'
    ccflags ='-D_REENTRANT -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/perl_1703310062586/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark=/usr/local/src/conda-prefix -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'undef/miniconda3/envs/bismark/lib/perl5/5.32/core_perl/Config_heavy.pl
    optimize='-O2'
    cppflags='--sysroot=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//x86_64-conda-linux-gnu/sysroot -D_REENTRANT -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/perl_1703310062586/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark=/usr/local/src/conda-prefix -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2'
    ccversion=''
    gccversion='12.3.0'
    gccosandvers=''
    intsize=4
    longsize=8
    ptrsize=8
    doublesize=8
    byteorder=12345678
    doublekind=3
    d_longlong=define
    longlongsize=8
    d_longdbl=define
    longdblsize=16
    longdblkind=3
    ivtype='long'
    ivsize=8
    nvtype='double'
    nvsize=8
    Off_t='off_t'
    lseeksize=8
    alignbytes=8
    prototype=define
  Linker and Libraries:
    ld='/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//bin/x86_64-conda-linux-gnu-gcc'
    ldflags ='-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib -Wl,-rpath-link,/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib -L/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib  -fstack-protector-strong'
    libpth=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/include-fixed /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//x86_64-conda-linux-gnu/sysroot/usr/lib /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//x86_64-conda-linux-gnu/sysroot/lib /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//x86_64-conda-linux-gnu/sysroot/lib64 /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//x86_64-conda-linux-gnu/sysroot/usr/lib64
    libs=-lpthread -ldl -lm -lcrypt -lutil -lc
    perllibs=-lpthread -ldl -lm -lcrypt -lutil -lc
    libc=
    so=so
    useshrplib=true
    libperl=libperl.so
    gnulibc_version='2.17'
  Dynamic Linking:
    dlsrc=dl_dlopen.xs
    dlext=so
    d_dlsymun=undef
    ccdlflags='-Wl,-E -Wl,-rpath,/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/../lib/perl5/5.32/core_perl/CORE'
    cccdlflags='-fPIC --sysroot=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//x86_64-conda-linux-gnu/sysroot'
    lddlflags='-shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib -Wl,-rpath-link,/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib -L/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib --sysroot=/home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/bin/..//x86_64-conda-linux-gnu/sysroot -fstack-protector-strong'


Characteristics of this binary (from libperl): 
  Compile-time options:
    HAS_TIMES
    MULTIPLICITY
    PERLIO_LAYERS
    PERL_COPY_ON_WRITE
    PERL_DONT_CREATE_GVSV
    PERL_IMPLICIT_CONTEXT
    PERL_MALLOC_WRAP
    PERL_OP_PARENT
    PERL_PRESERVE_IVUV
    USE_64_BIT_ALL
    USE_64_BIT_INT
    USE_ITHREADS
    USE_LARGE_FILES
    USE_LOCALE
    USE_LOCALE_COLLATE
    USE_LOCALE_CTYPE
    USE_LOCALE_NUMERIC
    USE_LOCALE_TIME
    USE_PERLIO
    USE_PERL_ATOF
    USE_REENTRANT_API
    USE_THREAD_SAFE_LOCALE
  Built under linux
  Compiled at Dec 23 2023 05:47:44
  @INC:
    /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib/perl5/5.32/site_perl
    /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib/perl5/site_perl
    /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib/perl5/5.32/vendor_perl
    /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib/perl5/vendor_perl
    /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib/perl5/5.32/core_perl
    /home/bioinformatics@zymoresearch.de/miniconda3/envs/bismark/lib/perl5/core_perl
    .

[mauke]

What do you mean by 'Set a directory path containing "@"'?

[ZRE-Services]

What do you mean by 'Set a directory path containing "@"'?

For reasons out of my control, on our ubuntu system the user folders within the home directory are named according to the users email adress (e.g. /home/bioinformatics@zymoresearch.de/) and therefore contain the symbol "@". When using Perl in this environment, the file Config_heavy.pl contains many directory paths that all start with "/home/bioinformatics@zymoresearch.de/". These paths are not correctly recognized as literal directory paths, but the contained "@" symbol seems to lead to the issue that "@zymoresearch" is recognized as a variable and not a string.

Please let me know if this is unclear still. I'll be happy to give futher details and to describe the workaround that i used to make things work for me

[mauke]

I created a path with a @ in it:

$ mkdir -p ~/tmp/hello@world
$ cd ~/tmp/hello@world

Then I used perl in this directory:

$ perl -wE 'say "hi"'
hi
$ pwd
/home/mauke/tmp/hello@world

No errors.

[ZRE-Services]

I should have recreated the bug reliably before opening the issue.
I was only able to recreate the issue using the package manager/virtual env tool conda (see below)
Feel free to close the issue, it might be better placed at conda or bowtie2

# install conda 
# create new conda environment within directory that contains "@"
(base) bioinformatics@zymo-hilde01:/home$ conda create -n perl_bug
# activate environment
(base) bioinformatics@zymo-hilde01:/home$ conda activate perl_bug
# install perl
(perl_bug) bioinformatics@zymo-hilde01:/home$ conda install perl
# install the popular DNA alignment tool bowtie2
(perl_bug) bioinformatics@zymo-hilde01:/home$ conda install bowtie2
# testing bowtie2 results in error message regarding Config_heavy.pl
(perl_bug) bioinformatics@zymo-hilde01:/home$ bowtie2 --help
Possible unintended interpolation of @zymoresearch in string at /home/bioinformatics@zymoresearch.de/miniconda3/envs/perl_bug/lib/perl5/5.32/core_perl/Config_heavy.pl line 246.
[...]
Global symbol "@zymoresearch" requires explicit package name (did you forget to declare "my @zymoresearch"?) at /home/bioinformatics@zymoresearch.de/miniconda3/envs/perl_bug/lib/perl5/5.32/core_perl/Config_heavy.pl line 246.

[jkeenan]

I should have recreated the bug reliably before opening the issue. I was only able to recreate the issue using the package manager/virtual env tool conda (see below) Feel free to close the issue, it might be better placed at conda or bowtie2

# install conda 
# create new conda environment within directory that contains "@"
(base) bioinformatics@zymo-hilde01:/home$ conda create -n perl_bug
# activate environment
(base) bioinformatics@zymo-hilde01:/home$ conda activate perl_bug
# install perl
(perl_bug) bioinformatics@zymo-hilde01:/home$ conda install perl
# install the popular DNA alignment tool bowtie2
(perl_bug) bioinformatics@zymo-hilde01:/home$ conda install bowtie2
# testing bowtie2 results in error message regarding Config_heavy.pl
(perl_bug) bioinformatics@zymo-hilde01:/home$ bowtie2 --help
Possible unintended interpolation of @zymoresearch in string at /home/bioinformatics@zymoresearch.de/miniconda3/envs/perl_bug/lib/perl5/5.32/core_perl/Config_heavy.pl line 246.
[...]
Global symbol "@zymoresearch" requires explicit package name (did you forget to declare "my @zymoresearch"?) at /home/bioinformatics@zymoresearch.de/miniconda3/envs/perl_bug/lib/perl5/5.32/core_perl/Config_heavy.pl line 246.

I downloaded a tarball of perl-5.40, unpacked it, and built it in a directory containing an @ sign.

$ sh ./Configure -des -Dprefix=/tmp/bioinformatics@zymoresearch.de && make install

I inspected the resulting ./lib/perl5/5.40.0/x86_64-linux/Config_heavy.pl.

$ grep -n 'prefix=' ./lib/perl5/5.40.0/x86_64-linux/Config_heavy.pl
248:config_arg2='-Dprefix=/tmp/bioinformatics@zymoresearch.de'
250:config_args='-des -Dprefix=/tmp/bioinformatics@zymoresearch.de'
1037:installprefix='/tmp/bioinformatics@zymoresearch.de'
1181:prefix='/tmp/bioinformatics@zymoresearch.de'
1265:siteprefix='/tmp/bioinformatics@zymoresearch.de'
1375:usevendorprefix='undef'
1401:vendorprefix=''

I then installed a couple of modules with the corresponding cpan. They installed correctly.

So I agree with you that the problem is not with perl. Closing. Thanks for the report.