This has me puzzled. This code worked on another server, but it's failing on Perl v5.8.8 with Date::Manip loaded from CPAN today.
Warning:
Use of uninitialized value in numeric lt (<) at /home/downside/lib/Date/Manip.pm line 3327.
at dailyupdate.pl line 13
main::__ANON__('Use of uninitialized value in numeric lt (<) at
/home/downsid...') called at
/home/downside/lib/Date/Manip.pm line 3327
Date::Manip::Date_SecsSince1970GMT(09, 16, 2008, 00, 21, 22) called at
/home/downside/lib/Date/Manip.pm line 1905
Date::Manip::UnixDate('today', '%Y-%m-%d') called at
TICKER/SYMBOLS/updatesymbols.pm line 122
TICKER::SYMBOLS::updatesymbols::getdate() called at
TICKER/SYMBOLS/updatesymbols.pm line 439
TICKER::SYMBOLS::updatesymbols::updatesymbol('DBI::db=HASH(0x87fcc34)',
'TICKER::SYMBOLS::symbol=HASH(0x8a43540)') called at
TICKER/SYMBOLS/updatesymbols.pm line 565
TICKER::SYMBOLS::updatesymbols::updatesymbols('DBI::db=HASH(0x87fcc34)', 1, 0, -1) called at
dailyupdate.pl line 149
EDGAR::updatesymbols('DBI::db=HASH(0x87fcc34)', 1, 0, -1) called at
dailyupdate.pl line 180
EDGAR::dailyupdate() called at dailyupdate.pl line 193
The code that's failing is simply:
sub getdate()
{ my $err; ## today
&Date::Manip::Date_Init('TZ=EST5EDT');
my $today = Date::Manip::UnixDate('today','%Y-%m-%d'); ## today's date
####print "Today is ",$today,"\n"; ## ***TEMP***
return($today);
}
That's right; Date::Manip is failing for "today".
The line in Date::Manip that is failing is:
my($tz)=$Cnf{"ConvTZ"};
$tz=$Cnf{"TZ"} if (! $tz);
$tz=$Zone{"n2o"}{lc($tz)} if ($tz !~ /^[+-]\d{4}$/);
my($tzs)=1;
$tzs=-1 if ($tz<0); ### ERROR OCCURS HERE
So Date::Manip is assuming that $Cnf has been initialized with elements "ConvTZ" or "TZ". Those are initialized in Date_Init, so that should have been taken care of.
It's only failing in my large program. If I just extract "getdate()" above
and run it standalone, there's no error. So there's something about the
global environment that affects this.
This seems to be a known, but not understood problem. If you search Google for
"Use of uninitialized value date manip" there are about 2400 hits.
This error has been reported with MythTV and grepmail.
It is a bug in Date::Manip version 5.48-5.54 for Win32. I've had difficulty with using standard/daylight variants of a timezones, e.g. 'EST5EDT', 'US/Eastern'. The only timezones that appear to work are those without daylight savings, e.g. 'EST'.
It is possible to turn off timezone conversion processing in the Date::Manip module:
Date::Manip::Date_Init("ConvTZ=IGNORE");
This will have undesired side-effects if you treat dates correctly. I would not use this workaround unless you are confident you will be never be processing dates from different timezones.
It's almost certain that your host doesn't have a definition for the timezone you're specifying, which is what's causing a value to be undefined.
Have you checked to make sure a TZ definition file of the same name actually exists on the host?
Date::Manip is supposed to be self-contained. It has a list of all its time zones in its own source, following "$zonesrfc=".
Can you try single-stepping through the debugger to see what exactly is going wrong? It could easily be %Zone that is wrong - %tz may be set correctly on line 1 or 2, but then the lookup on line 3 fails, ending up with undef.
Edit: %Date::Manip::Cnf and %Date::Manip::Zone are global variables, so you should be able to take a dump of them before and after the call to Date::Manip::Date_Init. If I read the source correctly %Cnf should contain a basic skeleton of configuration options before the call to Date_Init, and %Zone should be empty; after Date_Init, TZ should have your chosen value, and %Zone should be populated by a lookup table of time zones.
I see a reference to .DateManip.cnf in %Cnf, which might be something to look at - is it possible that you have such a file in your home directory, or the current working directory, which is overriding the default settings?
Related
I downloaded and set up PintOS and the dependencies on my home computer, but when I try to run pintos run alarm-multiple, I get the error:
Unrecognized character \x16; marked by <-- HERE after if ($<-- HERE near column 7 at ~/code/pintos/src/utils/pintos line 911.
That line has ^V on it, the synchronous idle control character. I haven't been able to find any information on this problem; it seems like I'm the only one experiencing it.
I have Perl v5.26.0 installed.
Use of literal control characters in variable names was deprecated in Perl 5.20:
Literal control characters in variable names
This deprecation affects things like $\cT, where \cT is a literal control (such as a NAK or NEGATIVE ACKNOWLEDGE character) in the source code. Surprisingly, it appears that originally this was intended as the canonical way of accessing variables like $^T, with the caret form only being added as an alternative.
The literal control form is being deprecated for two main reasons. It has what are likely unfixable bugs, such as $\cI not working as an alias for $^I, and their usage not being portable to non-ASCII platforms: While $^T will work everywhere, \cT is whitespace in EBCDIC. [perl #119123]
The code causing this problem was fixed in PintOS with this commit in 2016:
committer Ben Pfaff <blp#cs.stanford.edu>
Tue, 9 Feb 2016 04:47:10 +0000 (20:47 -0800)
Modern versions of Perl prefer a caret in variable names over literal
control characters and issue a warning if the control character is used.
This fixes the warning.
diff --git a/src/utils/pintos b/src/utils/pintos
index 1564216..2ebe642 100755 (executable)
--- a/src/utils/pintos
+++ b/src/utils/pintos
## -912,7 +912,7 ## sub get_load_average {
# Calls setitimer to set a timeout, then execs what was passed to us.
sub exec_setitimer {
if (defined $timeout) {
- if ($\16 ge 5.8.0) {
+ if ($^V ge 5.8.0) {
eval "
use Time::HiRes qw(setitimer ITIMER_VIRTUAL);
setitimer (ITIMER_VIRTUAL, $timeout, 0);
Perl 5.26 made it a fatal error to use literal control characters in variable names.
The way you fix it is by ensuring that you are using the most recent version of pintOS. The command git clone git://pintos-os.org/pintos-anon ought to do it.
^V is a perlvar. For reasons unknown to me, it was encoded not as ^ V, but as a single unicode character, which caused the program to fail.
Hi I was trying to use linkdatagen, which is a perl based tool. It requires a vcf file (using mpileup from SAMtools) and a hapmap annotation file (provided). I have followed the instructions but the moment I use the perl script provided, I get this error.
The codes I used are:
samtools mpileup -d10000 -q13 -Q13 -gf hg19.fa -l annotHapMap2U.txt samplex.bam | bcftools view -cg -t0.5 - > samplex.HM.vcf
Perl vcf2linkdatagen.pl -variantCaller mpileup -annotfile annotHapMap2U.txt -pop CEU -mindepth 10 -missingness 0 samplex.HM.vcf > samplex.brlmm
Use of uninitiated value $chr in concatenation (.) or string at vcf2linkdatagentest.pl line 487, <IN> line 1.... it goes on and on.. I have mailed the authors, and haven't heard from them yet. Can anyone here please help me? What am I doing wrong?
The perl script is :
http://bioinf.wehi.edu.au/software/linkdatagen/vcf2linkdatagen.pl
The HapMap file can be downloaded from the website mentioned below.
http://bioinf.wehi.edu.au/software/linkdatagen/
Thanks so much
Ignoring lines starting with #, vcf2linkdatagen.pl expects the first field of the first line of the VCF to contain something of the form "chrsomething", and your file doesn't meet that expectation. Examples from a comment in the code:
chr1 888659 . T C 226 . DP=26;AF1=1;CI95=1,1;DP4=0,0,9,17;MQ=49;FQ=-81 GT:PL:GQ 1/1:234,78,0:99
chr1 990380 . C . 44.4 . DP=13;AF1=7.924e-09;CI95=1.5,0;DP4=3,10,0,0;MQ=49;FQ=-42 PL 0
The warning means that a variable used in a string is not initialized (undefined). It is an indication that something might be wrong. The line in question can be traced to this statement
my $chr = $1 if ($tmp[0] =~ /chr([\S]+)/);
It is bad practice to use postfix if statements on a my statement.
As ikegami notes a workaround for this might be
my ($chr) = $tmp[0] =~ /chr([\S])/;
But since the match failed, it will likely return the same error. The only way to solve is to know more about the purpose of this variable, if the error should be fatal or not. The author has not handled this case, so we do not know.
If you want to know more about the problem, you might add a debug line such as this:
warn "'chr' value not found in the string '$tmp[0]'" unless defined $chr;
Typically, an error like this occurs when someone gives input to a program that the author did not expect. So if you see which lines give this warning, you might find out what to do about it.
I am trying to convert date from yymmdd to YYYY-MM-DD with Time::Piece module. With the input as Nov 31, 2000 (20001131), I am getting output as 2000-12-01. In reality, Nov 31 doesn't even exists.
use Time::Piece;
my $dt_str = Time::Piece->strptime('20001131', '%Y%m%d')->strftime('%Y-%m-%d');
print $dt_str;
Am I missing something here?
Internally, it does only rough validation and error reporting, and then performs the same transformations as POSIX::mktime does; any days beyond the end of a month will just cause it to advance the produced date into the next month. This does seem a little inconsistent; since it allows that for days, I'd also expect it to treat '20005931' as '2004-12-01', but instead it errors out.
I want to manage vendor branches in svn using the svn_load_dirs.pl script.
When I execute this script on my Mac OS X 10.5, perl v5.10.1 (*) built for darwin-multi-2level
I get he following error message:
Argument "2.07_02" isn't numeric in subroutine entry at /usr/local/bin/svn_load_dirs line 22.
What does this mean and is this harmful?
To understand Perl messages, you can look them up in perldoc perldiag:
Argument "%s" isn't numeric%s
(W numeric) The indicated string was
fed as an argument to an operator that
expected a numeric value instead.
Since this message is classified as a Warning, it may not be harmful. But, it is worth investigating. Since I do not have access to the svn_load_dirs.pl script, could you please update your Question with the 1st 22 lines of the script?
Cygwin user here (though if there's a suitable solution I will carry it over to K/Ubuntu, which I also use).
I have a Welcome message in my .bashrc that looks like the following:
SAD=(`date +%A-%B-%d-%Y`)
DUB=(`date -u +%k:%M`)
printf "Today's Date is: ${SAD}.\n"
printf "Dublin time is now ${DUB}. (24-Hour Clock)\n"
After numerous attempts to use whitespaces in the variable SAD above, I gave in and used hyphens. But I am, understandably, not satisfied with this band-aid solution. The problem, as I recall, was that every time I tried using quoted space, \s or some similar escape tag, along with the variables listed in the appropriate section of the GNU manpage for date, the variable for Year was either ignored or returned an error. What I do'nt want to have to do is resort to the full string as returned by date, but rather to keep the order in which I have things in the code above.
As I write this, it occurs to me that setting the IFS around this code for the Welcome message may work, provided I return it to defaults afterwards (the above appears at lines 13-17 of a 68-line .bashrc). However, I can't recall how to do that, nor am I sure that it would work.
Generally-speaking, .bashrc files are in valid BASH syntax, aren't they? Mine certainly resemble the scripts I've either written myself or tested from other sources. All I'm missing, I suppose, is the code for setting and unsetting the field separators around this message block.
No doubt anyone who comes up with a solution will be doing a favor not only to me, but to any other relative newbies on the Net taking their first (or thirteenth through seventeenth) steps in the world of shell scripting.
BZT
Putting
SAD=$(date "+%A %B %d %Y")
DUB=$(date -u +%k:%M)
echo "Today's Date is: ${SAD}."
echo "Dublin time is now ${DUB}. (24-Hour Clock)"
in my .bash_profile prints
Today's Date is: Thursday February 18 2010.
Dublin time is now 12:55. (24-Hour Clock)
I think that's what you want.
the problem is your array declaration.
SAD=(date +%A-%B-%d-%Y) just means you are putting the string "date" as element 0, and "+%A-%B-%d-%Y" as element 1. see for yourself
$ SAD=(date +%A-%B-%d-%Y) #<-- this is an array declaration
$ echo ${SAD[0]}
date
$ echo ${SAD[1]}
+%A-%B-%d-%Y
if you want the value of "date" command to be in a variable, use $(..), eg
$ SAD=$(date +%A-%B-%d-%Y)
$ echo ${SAD}
Thursday-February-18-2010
To get spaces, you need to quote the argument to date so that it's a single string. You're also erroneously declaring SAD and DUB as arrays, when what you really meant to do was evaluate them. Try this:
[/tmp]> $(date "+%A %B %d, %Y")
Thursday February 18, 2010
date +%A\ %B\ %d\ %Y
I found the combination that works:
SAD=$(date "+%A %B %d %Y")
echo $SAD
Thursday February 18 2010
Yet another instance when:
It pays to ask a question
It helps to know where to put your double quotes.
date obviously does not know from quoted space, but Bash does, so
it's a matter of "whispering in the right ear."
Thank you ghostdog74.
BZT