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  • Imputing missing data in aligned sequences

    - by Kwame Oduro
    I want a simple perl script that can help me impute missing nucleotides in aligned sequences: As an example, my old_file contains the following aligned sequences: seq1 ATGTC seq2 ATGTC seq3 ATNNC seq4 NNGTN seq5 CTCTN So I now want to infer all Ns in the file and get a new file with all the Ns inferred based on the majority nucleotide at a particular position. My new_file should look like this: seq1 ATGTC seq2 ATGTC seq3 ATGTC seq4 ATGTC seq5 CTCTC A script with usage: "impute_missing_data.pl old_file new_file" or any other approach will be helpful to me. Thank you.

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  • counting paragraphs in text file

    - by robjez
    I need to create perl code which allows counting paragraphs in text files. I tried this and doesn't work: open(READFILE, "<$filename") or die "could not open file \"$filename\":$!"; $paragraphs = 0; my($c); while($c = getc(READFILE)) { if($C ne"\n") { $paragraphs++; } } close(READFILE); print("Paragraphs: $paragraphs\n");

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  • Archive tar files to a different location inperl

    - by user314261
    Hi, I am a newbee in Perl. I am reading a directory having some archive files and uncompressing the archive files one by one. Everything seems well however the files are getting uncompressed in the folder which has the main perl code module which is running the sub modules. I want the archive to be generated in the folder I specify. This is my code: sub ExtractFile { #Read the folder which was copied in the output path recursively and extract if any file is compressed my $dirpath = $_[0]; opendir(D, "$dirpath") || die "Can't open dir $dirpath: $!\n"; my @list = readdir(D); closedir(D); foreach my $f (@list) { print " \$f = $f"; if(-f $dirpath."/$f") { #print " File in directory $dirpath \n ";#is \$f = $f\n"; my($file_name, $file_dirname,$filetype)= fileparse($f,qr{\..*}); #print " \nThe file extension is $filetype"; #print " \nThe file name is is $file_name"; # If compressed file then extract the file if($filetype eq ".tar" or $filetype eq ".tzr.gz") { my $arch_file = $dirpath."/$f"; print "\n file to be extracted is $arch_file"; my $tar = Archive::Tar->new($arch_file); #$tar->extract() or die ("Cannot extract file $arch_file"); #mkdir($dirpath."/$file_name"); $tar->extract_file($arch_file,$dirpath."/$file_name" ) or die ("Cannot extract file $arch_file"); } } if(-d $dirpath."/$f") { if($f eq "." or $f eq "..") { next; } print " Directory\n";# is $f"; ExtractFile($dirpath."/$f"); } } } The method ExtractFile is called recursively to loop all the archives. When using $tar-extract() it uncompresses in the folder which calls this metohd. when I use $tar-extract_file($arch_file,$dirpath."/$file_name" ) I get an error : No such file in archive: '/home/fsang/dante/workspace/output/s.tar' at /home/fsang/dante/lib/Extraction.pm line 80 Please help I have checked that path and input output there is no issue with it. Seems some usage problem I am not aware of for $tar-extract_file(). Many thanks for anyone resolving this issue. Regards, Sakshi

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  • How to use one script for diff and diff3 in Subversion?

    - by lamcro
    I have a perl script that determines what external diff to use depending on the file's content. I would like to use it determine external diff3 also. Which is the best method to know how my script is being called? I was planning to catch the last three parameters, and verify if they are all files, to use the diff3 options, but I'm hoping there is a cleaner method.

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  • How to pipe two CORE::system commands in a cross-platform way

    - by Pedro Silva
    I'm writing a System::Wrapper module to abstract away from CORE::system and the qx operator. I have a serial method that attempts to connect command1's output to command2's input. I've made some progress using named pipes, but POSIX::mkfifo is not cross-platform. Here's part of what I have so far (the run method at the bottom basically calls system): package main; my $obj1 = System::Wrapper->new( interpreter => 'perl', arguments => [-pe => q{''}], input => ['input.txt'], description => 'Concatenate input.txt to STDOUT', ); my $obj2 = System::Wrapper->new( interpreter => 'perl', arguments => [-pe => q{'$_ = reverse $_}'}], description => 'Reverse lines of input input', output => { '>' => 'output' }, ); $obj1->serial( $obj2 ); package System::Wrapper; #... sub serial { my ($self, @commands) = @_; eval { require POSIX; POSIX->import(); require threads; }; my $tmp_dir = File::Spec->tmpdir(); my $last = $self; my @threads; push @commands, $self; for my $command (@commands) { croak sprintf "%s::serial: type of args to serial must be '%s', not '%s'", ref $self, ref $self, ref $command || $command unless ref $command eq ref $self; my $named_pipe = File::Spec->catfile( $tmp_dir, int \$command ); POSIX::mkfifo( $named_pipe, 0777 ) or croak sprintf "%s::serial: couldn't create named pipe %s: %s", ref $self, $named_pipe, $!; $last->output( { '>' => $named_pipe } ); $command->input( $named_pipe ); push @threads, threads->new( sub{ $last->run } ); $last = $command; } $_->join for @threads; } #... My specific questions: Is there an alternative to POSIX::mkfifo that is cross-platform? Win32 named pipes don't work, as you can't open those as regular files, neither do sockets, for the same reasons. The above doesn't quite work; the two threads get spawned correctly, but nothing flows across the pipe. I suppose that might have something to do with pipe deadlocking or output buffering. What throws me off is that when I run those two commands in the actual shell, everything works as expected.

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  • How to use CPAN as a non-root user?

    - by juannavarroperez
    I want to install perl modules on a shared server on which I do not have root access. How can I do this? They also seem to have an older version of CPAN (it complains about that when running the command), is it possible to update the CPAN command being used from my account without requiring root access?

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  • How to handle main option with Getopt

    - by Jérôme
    I want to handle a feature which seems to me almost natural with programs, and I don't know how to handle it with Getopt perl package (no matter Std ot Long). I would like something like: ./perlscript <main option> [some options like -h or --output-file some_name] Options will be handled with - or --, but I want to be able to let the user give me the main and needed option without dashes. Is Getopt able to do that, or do I have to handle it by hand?

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  • How to keep same substrings in vim regex

    - by invisiblerhino
    Hi everyone. I'd ideally like a vim answer to this: I want to change [*, 1, *, *] to [*, 2, *, *] Here the stars refer to individual characters in the substring, which I would like to keep unchanged. For example [0, 1, 0, 1] to [0, 2, 0, 1] [1, 1, 1, 1] to [1, 2, 1, 1] If people know how to do this in perl or python or whatever, that would be equally good. Cheers

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  • Can I use a filehandle instead of a filename for creating DBM files?

    - by Dancrumb
    I'm using MLDBM to persist some Perl data structures and I'm wondering if there's an alternative to the following: tie %hash, "MLDBM", $dbm_file, O_CREAT | O_RDWR, 0644; Primarily, I'd like to be able to use STDOUT, rather than a known file name. This could then be redirected to a file on the shell-side. I've been searching with keywords like "tie", "DBM" and "filehandle", but the hits tend to talk about tying filehandles to things, as opposed to things to filehandles. Any suggestions?

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  • Remove duplicate characters and keep the uniq ones

    - by manu
    How do I remove duplicate characters and keep the uniq one only. Ex. My input is EFUAHUU UUUEUUUUH UJUJHHACDEFUCU Expected output is EFUAH UEH UJHACDEF I cam across perl -pe's/$1//gwhile/(.).*\/' which is wonderful but it is removing even the single occurence of the character in output. Can anyone help. Thanks in advance Manjeet

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  • Programming language for opengl screenshot software

    - by mandril
    I need to develop a multiplatform software that takes screenshots from opengl games without affecting the game in performance, it will run in the background and will add a watermark to my screenshots. What language should i use? I thought of Perl / Python. Anyone can point me out something to start? Thanks!

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  • Is there YAPE::Regex::Explain alternative to python?

    - by S.Mark
    Is there perl's YAPE::Regex::Explain alternative to python? Which could do \w+=\d+|\w+='[^']+' to explanations like this NODE EXPLANATION -------------------------------------------------------------------------------- \w+ word characters (a-z, A-Z, 0-9, _) (1 or more times (matching the most amount possible)) -------------------------------------------------------------------------------- = '=' -------------------------------------------------------------------------------- \d+ digits (0-9) (1 or more times (matching the most amount possible)) -------------------------------------------------------------------------------- | OR -------------------------------------------------------------------------------- \w+ word characters (a-z, A-Z, 0-9, _) (1 or more times (matching the most amount possible)) -------------------------------------------------------------------------------- =' '=\'' -------------------------------------------------------------------------------- [^']+ any character except: ''' (1 or more times (matching the most amount possible)) -------------------------------------------------------------------------------- ' '\''

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  • [Linux] Incremental search on command line?

    - by florianbw
    I'd like to write small scripts which feature incremental search (find-as-you-type) on the command line. Use case: I have my mobile phone connected via USB, Using gammu --sendsms TEXT I can write text messages. I have the phonebook as CSV, and want to search-as-i-type on that. What's the easiest/best way to do it? It might be in bash/zsh/perl/python or any other scripting language. Thanks!

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  • Can't seem to install imagick

    - by PolishHurricane
    I'm trying to install the PHP PEAR PECL extension "imagick" (image magick), but failing horribly. It seems that I keed installing packages to progress, but this one has me stumped. It seems to fail all the way at the bottom. Please Note: I'm using ArchLinux, apt-get doesn't save me. [root@Crux tmp]# pecl install imagick downloading imagick-3.0.1.tgz ... Starting to download imagick-3.0.1.tgz (93,920 bytes) .....................done: 93,920 bytes 13 source files, building running: phpize Configuring for: PHP Api Version: 20100412 Zend Module Api No: 20100525 Zend Extension Api No: 220100525 Please provide the prefix of Imagemagick installation [autodetect] : building in /tmp/pear/temp/pear-build-rootLbSUWT/imagick-3.0.1 running: /tmp/pear/temp/imagick/configure --with-imagick checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for a sed that does not truncate output... /bin/sed checking for cc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking how to run the C preprocessor... cc -E checking for icc... no checking for suncc... no checking whether cc understands -c and -o together... yes checking for system library directory... lib checking if compiler supports -R... no checking if compiler supports -Wl,-rpath,... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu checking for PHP prefix... /usr checking for PHP includes... -I/usr/include/php -I/usr/include/php/main -I/usr/include/php/TSRM -I/usr/include/php/Zend -I/usr/include/php/ext -I/usr/include/php/ext/date/lib checking for PHP extension directory... /usr/lib/php/modules checking for PHP installed headers prefix... /usr/include/php checking if debug is enabled... no checking if zts is enabled... no checking for re2c... re2c checking for re2c version... 0.13.5 (ok) checking for gawk... gawk checking whether to enable the imagick extension... yes, shared checking whether to enable the imagick GraphicsMagick backend... no checking ImageMagick MagickWand API configuration program... found in /usr/bin/MagickWand-config checking if ImageMagick version is at least 6.2.4... found version 6.7.8 Q16 checking for MagickWand.h header file... found in /usr/include/ImageMagick/wand/MagickWand.h checking PHP version is at least 5.1.3... yes. found 5.4.6 checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking whether ln -s works... yes checking how to recognize dependent libraries... pass_all checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking the maximum length of command line arguments... 1572864 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no creating libtool appending configuration tag "CXX" to libtool configure: creating ./config.status config.status: creating config.h running: make /bin/sh /tmp/pear/temp/pear-build-rootLbSUWT/imagick-3.0.1/libtool --mode=compile cc -I. -I/tmp/pear/temp/imagick -DPHP_ATOM_INC -I/tmp/pear/temp/pear-build-rootLbSUWT/imagick-3.0.1/include -I/tmp/pear/temp/pear-build-rootLbSUWT/imagick-3.0.1/main -I/tmp/pear/temp/imagick -I/usr/include/php -I/usr/include/php/main -I/usr/include/php/TSRM -I/usr/include/php/Zend -I/usr/include/php/ext -I/usr/include/php/ext/date/lib -I/usr/include/ImageMagick -DHAVE_CONFIG_H -g -O2 -c /tmp/pear/temp/imagick/imagick_class.c -o imagick_class.lo mkdir .libs cc -I. -I/tmp/pear/temp/imagick -DPHP_ATOM_INC -I/tmp/pear/temp/pear-build-rootLbSUWT/imagick-3.0.1/include -I/tmp/pear/temp/pear-build-rootLbSUWT/imagick-3.0.1/main -I/tmp/pear/temp/imagick -I/usr/include/php -I/usr/include/php/main -I/usr/include/php/TSRM -I/usr/include/php/Zend -I/usr/include/php/ext -I/usr/include/php/ext/date/lib -I/usr/include/ImageMagick -DHAVE_CONFIG_H -g -O2 -c /tmp/pear/temp/imagick/imagick_class.c -fPIC -DPIC -o .libs/imagick_class.o /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getimagematteâ: /tmp/pear/temp/imagick/imagick_class.c:268:2: warning: âMagickGetImageMatteâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:82) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getsizeoffsetâ: /tmp/pear/temp/imagick/imagick_class.c:406:2: warning: passing argument 2 of âMagickGetSizeOffsetâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:87:3: note: expected âssize_t *â but argument is of type âlong int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_paintfloodfillimageâ: /tmp/pear/temp/imagick/imagick_class.c:1016:3: warning: âMagickPaintFloodfillImageâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:99) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c:1019:3: warning: âMagickPaintFloodfillImageâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:99) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getimagepropertiesâ: /tmp/pear/temp/imagick/imagick_class.c:1083:2: warning: passing argument 3 of âMagickGetImagePropertiesâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:35:5: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getimageprofilesâ: /tmp/pear/temp/imagick/imagick_class.c:1131:2: warning: passing argument 3 of âMagickGetImageProfilesâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:33:5: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_recolorimageâ: /tmp/pear/temp/imagick/imagick_class.c:1402:2: warning: âMagickRecolorImageâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:109) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_setfontâ: /tmp/pear/temp/imagick/imagick_class.c:1442:3: error: âstruct _php_core_globalsâ has no member named âsafe_modeâ /tmp/pear/temp/imagick/imagick_class.c:1442:3: error: âCHECKUID_CHECK_FILE_AND_DIRâ undeclared (first use in this function) /tmp/pear/temp/imagick/imagick_class.c:1442:3: note: each undeclared identifier is reported only once for each function it appears in /tmp/pear/temp/imagick/imagick_class.c:1442:3: error: âCHECKUID_NO_ERRORSâ undeclared (first use in this function) /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_queryformatsâ: /tmp/pear/temp/imagick/imagick_class.c:2580:2: warning: passing argument 2 of âMagickQueryFormatsâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:41:5: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_queryfontsâ: /tmp/pear/temp/imagick/imagick_class.c:2607:2: warning: passing argument 2 of âMagickQueryFontsâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:40:5: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_colorfloodfillimageâ: /tmp/pear/temp/imagick/imagick_class.c:3396:2: warning: âMagickColorFloodfillImageâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:75) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_mapimageâ: /tmp/pear/temp/imagick/imagick_class.c:3730:2: warning: âMagickMapImageâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:86) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_mattefloodfillimageâ: /tmp/pear/temp/imagick/imagick_class.c:3763:2: warning: âMagickMatteFloodfillImageâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:88) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_medianfilterimageâ: /tmp/pear/temp/imagick/imagick_class.c:3790:2: warning: âMagickMedianFilterImageâ is deprecated (declared at /usr/include/ImageMagick/wand/magick-image.h:217) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_paintopaqueimageâ: /tmp/pear/temp/imagick/imagick_class.c:3853:2: warning: âMagickPaintOpaqueImageChannelâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:104) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_painttransparentimageâ: /tmp/pear/temp/imagick/imagick_class.c:3916:2: warning: âMagickPaintTransparentImageâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:107) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_reducenoiseimageâ: /tmp/pear/temp/imagick/imagick_class.c:4059:2: warning: âMagickReduceNoiseImageâ is deprecated (declared at /usr/include/ImageMagick/wand/magick-image.h:266) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getimageattributeâ: /tmp/pear/temp/imagick/imagick_class.c:5068:2: warning: âMagickGetImageAttributeâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:59) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getimagechannelextremaâ: /tmp/pear/temp/imagick/imagick_class.c:5253:2: warning: âMagickGetImageChannelExtremaâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:78) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c:5253:2: warning: passing argument 3 of âMagickGetImageChannelExtremaâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:68:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/deprecate.h:78:3: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c:5253:2: warning: passing argument 4 of âMagickGetImageChannelExtremaâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:68:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/deprecate.h:78:3: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getimageextremaâ: /tmp/pear/temp/imagick/imagick_class.c:5506:2: warning: âMagickGetImageExtremaâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:80) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c:5506:2: warning: passing argument 2 of âMagickGetImageExtremaâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:68:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/deprecate.h:80:3: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c:5506:2: warning: passing argument 3 of âMagickGetImageExtremaâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:68:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/deprecate.h:80:3: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getimagehistogramâ: /tmp/pear/temp/imagick/imagick_class.c:5629:2: warning: passing argument 2 of âMagickGetImageHistogramâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:74:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-image.h:415:5: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getimagepageâ: /tmp/pear/temp/imagick/imagick_class.c:5740:2: warning: passing argument 2 of âMagickGetImagePageâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:74:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-image.h:192:3: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c:5740:2: warning: passing argument 3 of âMagickGetImagePageâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:74:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-image.h:192:3: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c:5740:2: warning: passing argument 4 of âMagickGetImagePageâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:74:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-image.h:192:3: note: expected âssize_t *â but argument is of type âlong int *â /tmp/pear/temp/imagick/imagick_class.c:5740:2: warning: passing argument 5 of âMagickGetImagePageâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:74:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-image.h:192:3: note: expected âssize_t *â but argument is of type âlong int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getimageindexâ: /tmp/pear/temp/imagick/imagick_class.c:6344:2: warning: âMagickGetImageIndexâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:65) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_setimageindexâ: /tmp/pear/temp/imagick/imagick_class.c:6369:2: warning: âMagickSetImageIndexâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:113) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getimagesizeâ: /tmp/pear/temp/imagick/imagick_class.c:6447:2: warning: âMagickGetImageSizeâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:140) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_setimageattributeâ: /tmp/pear/temp/imagick/imagick_class.c:6796:2: warning: âMagickSetImageAttributeâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:111) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_flattenimagesâ: /tmp/pear/temp/imagick/imagick_class.c:7043:2: warning: âMagickFlattenImagesâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:132) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_averageimagesâ: /tmp/pear/temp/imagick/imagick_class.c:8079:2: warning: âMagickAverageImagesâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:131) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_mosaicimagesâ: /tmp/pear/temp/imagick/imagick_class.c:8516:2: warning: âMagickMosaicImagesâ is deprecated (declared at /usr/include/ImageMagick/wand/deprecate.h:135) [-Wdeprecated-declarations] /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getpageâ: /tmp/pear/temp/imagick/imagick_class.c:9126:2: warning: passing argument 2 of âMagickGetPageâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:84:3: note: expected âsize_t *â but argument is of type âlong int *â /tmp/pear/temp/imagick/imagick_class.c:9126:2: warning: passing argument 3 of âMagickGetPageâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:84:3: note: expected âsize_t *â but argument is of type âlong int *â /tmp/pear/temp/imagick/imagick_class.c:9126:2: warning: passing argument 4 of âMagickGetPageâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:84:3: note: expected âssize_t *â but argument is of type âlong int *â /tmp/pear/temp/imagick/imagick_class.c:9126:2: warning: passing argument 5 of âMagickGetPageâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:84:3: note: expected âssize_t *â but argument is of type âlong int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getquantumdepthâ: /tmp/pear/temp/imagick/imagick_class.c:9154:2: warning: passing argument 1 of âMagickGetQuantumDepthâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:52:4: note: expected âsize_t *â but argument is of type âlong int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getquantumrangeâ: /tmp/pear/temp/imagick/imagick_class.c:9176:2: warning: passing argument 1 of âMagickGetQuantumRangeâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:53:4: note: expected âsize_t *â but argument is of type âlong int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getsamplingfactorsâ: /tmp/pear/temp/imagick/imagick_class.c:9247:2: warning: passing argument 2 of âMagickGetSamplingFactorsâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:59:4: note: expected âsize_t *â but argument is of type âlong int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getsizeâ: /tmp/pear/temp/imagick/imagick_class.c:9273:2: warning: passing argument 2 of âMagickGetSizeâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:86:3: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c:9273:2: warning: passing argument 3 of âMagickGetSizeâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:86:3: note: expected âsize_t *â but argument is of type âlong unsigned int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_getversionâ: /tmp/pear/temp/imagick/imagick_class.c:9299:2: warning: passing argument 1 of âMagickGetVersionâ from incompatible pointer type [enabled by default] In file included from /usr/include/ImageMagick/wand/MagickWand.h:73:0, from /tmp/pear/temp/imagick/php_imagick.h:49, from /tmp/pear/temp/imagick/imagick_class.c:21: /usr/include/ImageMagick/wand/magick-property.h:55:4: note: expected âsize_t *â but argument is of type âlong int *â /tmp/pear/temp/imagick/imagick_class.c: In function âzim_imagick_setimageprogressmonitorâ: /tmp/pear/temp/imagick/imagick_class.c:9534:2: error: âstruct _php_core_globalsâ has no member named âsafe_modeâ /tmp/pear/temp/imagick/imagick_class.c:9534:2: error: âCHECKUID_CHECK_FILE_AND_DIRâ undeclared (first use in this function) /tmp/pear/temp/imagick/imagick_class.c:9534:2: error: âCHECKUID_NO_ERRORSâ undeclared (first use in this function) make: *** [imagick_class.lo] Error 1 ERROR: `make' failed

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