CVS commit: pkgsrc/devel/cfitsio

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/devel/cfitsio
From: "Makoto Fujiwara" <mef%netbsd.org@localhost>
Date: Sat, 23 Nov 2019 06:58:14 +0000

Module Name:    pkgsrc
Committed By:   mef
Date:           Sat Nov 23 06:58:14 UTC 2019

Modified Files:
        pkgsrc/devel/cfitsio: Makefile PLIST distinfo
        pkgsrc/devel/cfitsio/patches: patch-aa

Log Message:
(devel/cfitsio) Updated 3.390 to 3.450

(from docs/changes.txt), sorry for long lines.
Version 3.45 - May 2018

  - New support for reading and writing unsigned long long datatypes.
    This includes 'implicit datatype conversion' between the unsigned long
    long datatype and all the other datatypes.

  - Increased the hardcoded NMAXFILES setting for maximum number of
    open files from 1000 to 10000.

  - Bug fix to fits_calc_binning wrapper function, which wasn't filling
    in the returned float variables.

  - Fixed a parsing bug for image subsection and column binning range
    specifiers that was introduced in v3.44.

Version 3.44 - April 2018

  - This release primarily patches security vulnerabilities.  We
    strongly encourage this upgrade, particularly for those running
    CFITSIO in web accessible applications.

    In addition, the following enhancements and fixes were made:

  - Enhancement to 'template' and 'colfilter' functionality.  It is now
    possible to delete multiple keywords using wildcard syntax. See
    "Column and Keyword Filtering Specification" section of manual for
    details.

  - histo.c uses double precision internally for all floating point
    binning; new double-precision subroutines fits_calc_binningd(),
    fits_rebin_wcsd(), and fits_make_histd(); existing
    single-precision histogram functions still work but convert values
    to double-precision internally.

  - new subroutine fits_copy_cols() / ffccls() to copy multiple columns

  - Fix in imcompress.c for HCOMPRESS and PLIO compression of unsigned
    short integers.

  - Fix to fits_insert_card(ffikey).  It had wrongly been capitalizing
    letters that appeared before an '=' sign on a CONTINUE line.

Version 3.43 - March 2018

The NASA security team requires the following warning to all users of
CFITSIO:

   =====
   The CFITSIO open source software project contains vulnerabilities
   that could allow a remote, unauthenticated attacker to take control
   of a server running the CFITSIO software.  These vulnerabilities
   affect all servers and products running the CFITSIO software.

   The CFITSIO team has released software updates to address these
   vulnerabilities.  There are no workarounds to address these
   vulnerabilities.  In all cases, the CFITSIO team is recommending an
   immediate update to resolve the issues.
   =====

  - Fixed security vulnerabilities.

  - Calls to https driver functions in cfileio.c need to be macro-
     protected by the HAVE_NET_SERVICES variable (as are the http and
     ftp driver function calls).  Otherwise CMake builds on native
     Windows will fail since drvrnet.o is left empty.

   - Bug fix to ffmvec function.  Should be resetting a local colptr
     variable after making a call to ffiblk (which can reallocate Ftpr->
     tableptr).  Originally reported by Willem van Straten.

   - Ignore any attempted request to not quantize an image before
     compressing it if the image has integer datatype pixels.

   - Improved error message construction throughout CFITSIO.

Version 3.42 - August 2017 (Stand-alone release)

   - added https support to the collection of drivers handled in cfileio.c
     and drvrnet.c.  This also handles the case where http transfers are
     rerouted to https.  Note that this enhancement introduces a dependency
     on the libcurl development package.  If this package is absent, CFITSIO
     will still build but will not have https capability.

   - made fix to imcomp_init_table function in imcompress.c.  It now writes
     ZSIMPLE keyword only to a compressed image that will be placed in the
     primary header.

   - fix made to fits_get_col_display_width for case of a vector column
     of strings.

Version 3.42 - March 2017 (Ftools release only)

   - in ftp_open_network and in ftp_file_exist, added code to repeatedly
     attempt to make a ftp connection if the ftp server does not respond
     to the first request. (some ftp servers don't appear to be 100% reliable).

   - in drvrnet.c added many calls to 'fclose' to close unneeded files,
     to avoid exceeding the maximum allowed number of files that can be
     open at once.

   - made substantial changes to the ftp_checkfile and http_checkfile routines
     to streamline the process of checking for the existence of a .gz or .Z
     compressed version of the file before opening the uncompressed file
     (when using http or ftp to open the file).

   - modified the code in ftp_open_network to send "\r\n" as end-of-line
     characters instead of just "\n".  Some ftp servers (in particular,
     at heasarc.gsfc.nasa.gov) now require both characters, otherwise the
     network connection simply hangs.

   - modified the http_open_network routine to handle HTTP 301 or 302 redirects
     to a FTP url.  This is needed to support the new configuration on
     the heasarc HTTP server which sometimes redirects http URLS to a ftp URL.

Version 3.41 - November 2016

   - The change made in version 3.40 to include strings.h caused problems on
     Windows (and other) platforms, so this change was backed out. The reason
     for including it was to define the strcasecmp and strcasencmp functions, so
     as an alternative, new equivalent functions called fits_strcasecmp and
     fits_strncasecmp have been added to CFITSIO.as a substitute. All the
     previous calls to the str[n]casecmp functions have been changed to
     now call fits_str[n]casecmp. In addition, the previously defined
     ngp_strcasecmp function (in grparser.c) has been removed and the calls to
     it have been changed to fits_strcasecmp.

   - The speed.c utility program was changed to correctly call
     the gettimeofday function with a NULL second arguement.

Version 3.40 - October 2016

   - fixed a bug when writing long string keywords with the CONTINUE convention
     which caused the CONTINUE'd strings to only be 16 characters long, instead
     of using up all the available space in the 80-character header record.

   - fixed a missing 'defined' keyword in fitsio.h.

   - replaced all calls to strtok (which is not threadsafe) with a new ffstrtok
     function which internally calls the threadsafe strtok_r function.  One
     byproduct of this change is that <strings.h> must also be included
     in several of the C source code files.

   - modified the ffphbn function in putkey.c to support TFORM specifiers that
     use lowercase 'p' (instead of uppercase) when referring to a variable-length
     array column.

   - modified the lexical parser in eval.y and eval_y.c to support bit array
     columns (with TFORMn = 'X') with greater than 256 elements. Fix to bitcmp
     function:  The internal 'stream' array is now
     allocated dynamically rather than statically fixed at size 256.
     This was failing when users attempted a row filtering of a bitcol
     that was wider than 256X. In bitlgte, bitand, and bitor functions, replaced
     static stream[256] array allocation with dynamic allocation.

   - modified the ffiter function in putcol.c to fix a problem which could
     cause the iterator function to incorrectly deal with null values.  This
     only affected TLONG type columns in cases where sizeof(long) = 8, as well
     as for TLONGLONG type columns.

   - Fix made to uncompress2mem function in zcomprss.c for case where output
     uncompressed file expands to over the 2^32 (4Gb) limit.  It now
     checks for this case at the start, and implements a 4Gb paging
     system through the output buffer.  The problem was specifically
     caused by the d_stream.avail_out member being of 4-byte type uInt,
     and thus unable to handle any memory position values above 4Gb.

   - fixed a bug in fpackutil.c when using the -i2f (integer to float) option
     in fpack to compress an integer image that is scaled with non-default values
     for BSCALE and BZERO. This required an additional call to ffrhdu to reset
     the internal structures that describe the input FITS file.

   - modified fits_uncompress_table in imcompress.c to silently ignore the
     ZTILELEN keyword value if it larger than the number of rows in the table

   - Tweak strcasecmp/strncasecmp ifdefs to exclude 64-bit MINGW
     environment, as it does not lack those functions. (eval_l.c,
     fitsio2.h)

   - CMakeLists.txt: Set M_LIB to "" for MINGW build environment (in
     addition to MSVC).

   - Makefile.in: Add *.dSYM (non-XCode gcc leftovers on Macs) to
     clean list.  Install libs by name rather than using a wildcard.

   - configure: Fix rpath token usage for XCode vs. non-XCode gcc on Macs.


To generate a diff of this commit:
cvs rdiff -u -r1.32 -r1.33 pkgsrc/devel/cfitsio/Makefile
cvs rdiff -u -r1.9 -r1.10 pkgsrc/devel/cfitsio/PLIST
cvs rdiff -u -r1.14 -r1.15 pkgsrc/devel/cfitsio/distinfo
cvs rdiff -u -r1.6 -r1.7 pkgsrc/devel/cfitsio/patches/patch-aa

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/devel/cfitsio/Makefile
diff -u pkgsrc/devel/cfitsio/Makefile:1.32 pkgsrc/devel/cfitsio/Makefile:1.33
--- pkgsrc/devel/cfitsio/Makefile:1.32  Tue Aug  1 14:58:54 2017
+++ pkgsrc/devel/cfitsio/Makefile       Sat Nov 23 06:58:14 2019
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.32 2017/08/01 14:58:54 wiz Exp $
+# $NetBSD: Makefile,v 1.33 2019/11/23 06:58:14 mef Exp $
 
-DISTNAME=      cfitsio3390
+DISTNAME=      cfitsio3450
 PKGNAME=       ${DISTNAME:S/o3/o-3./}
-PKGREVISION=   1
 CATEGORIES=    devel
 MASTER_SITES=  http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/
 
@@ -25,7 +24,7 @@ BUILD_TARGET= all testprog
 
 INSTALLATION_DIRS=     include lib lib/pkgconfig share/doc/cfitsio
 
-CFITSIO_DOCS=  cfitsio.pdf cfitsio.doc cfortran.doc fitsio.pdf fitsio.doc \
+CFITSIO_DOCS=  cfitsio.pdf cfortran.doc fitsio.pdf fitsio.doc \
                fpackguide.pdf quick.pdf
 
 post-build:
@@ -40,4 +39,5 @@ post-install:
        cd ${WRKSRC}/docs; \
        ${INSTALL_DATA} ${CFITSIO_DOCS} ${DESTDIR}${PREFIX}/share/doc/cfitsio
 
+.include "../../www/curl/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/devel/cfitsio/PLIST
diff -u pkgsrc/devel/cfitsio/PLIST:1.9 pkgsrc/devel/cfitsio/PLIST:1.10
--- pkgsrc/devel/cfitsio/PLIST:1.9      Sun Jun 19 07:40:17 2016
+++ pkgsrc/devel/cfitsio/PLIST  Sat Nov 23 06:58:14 2019
@@ -1,11 +1,10 @@
-@comment $NetBSD: PLIST,v 1.9 2016/06/19 07:40:17 markd Exp $
+@comment $NetBSD: PLIST,v 1.10 2019/11/23 06:58:14 mef Exp $
 include/drvrsmem.h
 include/fitsio.h
 include/fitsio2.h
 include/longnam.h
 lib/libcfitsio.la
 lib/pkgconfig/cfitsio.pc
-share/doc/cfitsio/cfitsio.doc
 share/doc/cfitsio/cfitsio.pdf
 share/doc/cfitsio/cfortran.doc
 share/doc/cfitsio/fitsio.doc

Index: pkgsrc/devel/cfitsio/distinfo
diff -u pkgsrc/devel/cfitsio/distinfo:1.14 pkgsrc/devel/cfitsio/distinfo:1.15
--- pkgsrc/devel/cfitsio/distinfo:1.14  Sat Jun 18 09:06:11 2016
+++ pkgsrc/devel/cfitsio/distinfo       Sat Nov 23 06:58:14 2019
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.14 2016/06/18 09:06:11 mef Exp $
+$NetBSD: distinfo,v 1.15 2019/11/23 06:58:14 mef Exp $
 
-SHA1 (cfitsio3390.tar.gz) = 818ee00793ae27dfc75752c2415d0a7230ad5066
-RMD160 (cfitsio3390.tar.gz) = 515146dd69dfacc0a41f5d2727332c81b9fa501b
-SHA512 (cfitsio3390.tar.gz) = 9e72fe58e1b2e45dfad23c5a60f9056a4e958b3b567751c5284d5d89992f0a2721aa44ede8655f0e1595eaea9d6ba4644b001c54274764f9d05f890d471e4534
-Size (cfitsio3390.tar.gz) = 4755390 bytes
-SHA1 (patch-aa) = cacbc44cd442096d094faef79a2bb47980df8543
+SHA1 (cfitsio3450.tar.gz) = 85b4adeba79a7691114695e6bafd6d968e68c21f
+RMD160 (cfitsio3450.tar.gz) = 1a421eeaed9a511e76533aa457dbd44002d23627
+SHA512 (cfitsio3450.tar.gz) = f553f9bbedc3ffabf939bb507d3c41d6dc0d889b3a0835c23a7aff90ba98d7f9a6217527d69bc8984ce9bd9664681baeec5b1555d2ab51aaca003fdb5a08127e
+Size (cfitsio3450.tar.gz) = 4738748 bytes
+SHA1 (patch-aa) = e10b375b3d62a1c1f29a38db6d02ffc89c1c40e8
 SHA1 (patch-ad) = 761aedc2ae885c119ac2726ba89aaa7c193a8834

Index: pkgsrc/devel/cfitsio/patches/patch-aa
diff -u pkgsrc/devel/cfitsio/patches/patch-aa:1.6 pkgsrc/devel/cfitsio/patches/patch-aa:1.7
--- pkgsrc/devel/cfitsio/patches/patch-aa:1.6   Sat Jun 18 09:06:11 2016
+++ pkgsrc/devel/cfitsio/patches/patch-aa       Sat Nov 23 06:58:14 2019
@@ -1,10 +1,10 @@
-$NetBSD: patch-aa,v 1.6 2016/06/18 09:06:11 mef Exp $
+$NetBSD: patch-aa,v 1.7 2019/11/23 06:58:14 mef Exp $
 
 Use libtool.
 
---- Makefile.in.orig   2016-04-02 04:06:28.000000000 +0900
-+++ Makefile.in        2016-06-18 17:30:44.000000000 +0900
-@@ -37,14 +37,15 @@ INSTALL_DIRS       = @INSTALL_ROOT@ ${CFITSIO_
+--- Makefile.in.orig   2018-05-10 04:16:01.000000000 +0900
++++ Makefile.in        2019-11-23 15:43:52.872488997 +0900
+@@ -36,14 +36,15 @@ INSTALL_DIRS       = @INSTALL_ROOT@ ${CFITSIO_
  SHELL =               /bin/sh
  ARCHIVE =     @ARCHIVE@
  RANLIB =      @RANLIB@
@@ -22,7 +22,7 @@ Use libtool.
  LIBS =                @LIBS@
  FLEX =                flex
  BISON =               bison
-@@ -94,11 +95,11 @@ all:
+@@ -93,11 +94,11 @@ all:
  all-nofitsio:
                ${MAKE} stand_alone "FITSIO_SRC="
  
@@ -38,22 +38,30 @@ Use libtool.
  
  shared: lib${PACKAGE}${SHLIB_SUFFIX}
  
-@@ -109,10 +110,10 @@ lib${PACKAGE}${SHLIB_SUFFIX}: ${OBJECTS}
+@@ -108,16 +109,17 @@ lib${PACKAGE}${SHLIB_SUFFIX}: ${OBJECTS}
                        ln -sf ${CFITSIO_SHLIB_SONAME} $@; \
                fi
  
 -install:      lib${PACKAGE}.a ${INSTALL_DIRS}
--              /bin/cp -a lib${PACKAGE}* ${CFITSIO_LIB}
--              /bin/cp fitsio.h fitsio2.h longnam.h drvrsmem.h ${CFITSIO_INCLUDE}
--              /bin/cp cfitsio.pc ${CFITSIO_LIB}/pkgconfig
+-              @for lib in lib${PACKAGE}.a lib${PACKAGE}${SHLIB_SUFFIX} \
 +install:      lib${PACKAGE}.la ${INSTALL_DIRS}
 +              ${LIBTOOL} --mode=install ${BSD_INSTALL_LIB} libcfitsio.la ${CFITSIO_LIB}
-+              ${BSD_INSTALL_DATA} fitsio.h fitsio2.h longnam.h drvrsmem.h ${CFITSIO_INCLUDE}/
++              @for lib in  lib${PACKAGE}${SHLIB_SUFFIX} \
+                               ${CFITSIO_SHLIB} ${CFITSIO_SHLIB_SONAME}; do \
+                   if [ -f $$lib ]; then \
+                       echo "/bin/cp -a $$lib ${CFITSIO_LIB}"; \
+-                      /bin/cp -a $$lib ${CFITSIO_LIB}; \
++                      ${BSD_INSTALL_DATA} -a $$lib ${CFITSIO_LIB}; \
+                   fi; \
+               done
+-              /bin/cp fitsio.h fitsio2.h longnam.h drvrsmem.h ${CFITSIO_INCLUDE}
+-              /bin/cp cfitsio.pc ${CFITSIO_LIB}/pkgconfig
++              ${BSD_INSTALL_DATA} fitsio.h fitsio2.h longnam.h drvrsmem.h ${CFITSIO_INCLUDE}
 +              ${BSD_INSTALL_DATA} cfitsio.pc ${CFITSIO_LIB}/pkgconfig
                @for task in ${FPACK_UTILS} ${UTILS}; do \
                    if [ -f $$task ]; then \
                        if [ ! -d ${CFITSIO_BIN} ]; then mkdir -p ${CFITSIO_BIN}; fi; \
-@@ -133,29 +134,29 @@ utils:           ${FPACK_UTILS} ${UTILS}
+@@ -138,29 +140,29 @@ utils:           ${FPACK_UTILS} ${UTILS}
  swapproc.o:   swapproc.c
                ${CC} -c ${CFLAGS} ${CPPFLAGS} ${SSE_FLAGS} ${DEFS} $<

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