search for: xzfile

Dear guangchuang, I was stopped by the following error when using Package: clusterProfiler on R 2.15.3 on windows 7. Error in xzfile(file, “wb”, compression = 9) : Cannot open the connection In addition: warning message: cannot initialize lzma encoder, error 5 The too functions: Gff2GeneTable() and buildGOmap() are not working because of this error. Could you please let me know how to fix these error. [source of the package:...

...ught up to that (RHEL 6 and FreeBSD 10 support SOCK_CLOEXEC, for example), and we're doing ourselves a disservice by using silent fallback instead of actively detecting with compile failure on systems that are still behind. [1] http://austingroupbugs.net/view.php?id=411 Conflicts: filters/xz/xzfile.c - The fallback moved from plugins/xz/xzfile.c (and in fact has been dead code since commit c879d310 made it a filter) plugins/file/file.c - context changes in the meantime src/internal.h - Moved to server/internal.h --- server/internal.h | 8 -------- filters/xz/xzfile.c...

...documenting at each site that prefers to use the new interfaces whether the use is essential or merely reducing lines of code, for the sake of systems that are behind in atomic support. [1] https://dev.haiku-os.org/ticket/15219 [2] http://austingroupbugs.net/view.php?id=411 Conflicts: filters/xz/xzfile.c - The fallback moved from plugins/xz/xzfile.c (and in fact has been dead code since commit c879d310 made it a filter) plugins/file/file.c - context changes in the meantime src/internal.h - Moved to server/internal.h plugins/split/split.c - Not in the original patch; copied in 9ad64ba5 --- ser...

v2: - Fixes a number of bugs in corner cases. - Uses a 1M block size to fetch from the underlying plugin. This improves performance considerably. I also tested this much more thoroughly and can't find any more bugs. Rich.

Matt asked if xz should really be a filter rather than a plugin. The answer is yes, of course it should be! That's been something in the todo file for a while. The commit converts the xz plugin code into a filter (leaving the plugin around, but deprecating it). plugin: nbdkit xz file.xz filter: nbdkit --filter=xz file file.xz plugin: # can't be done filter: nbdkit

...LOEXEC on fds server/internal.h | 8 ---- filters/cache/blk.c | 19 ++++++++- filters/cow/blk.c | 19 ++++++++- filters/log/log.c | 20 ++++++++- filters/rate/rate.c | 26 ++++++++---- filters/stats/stats.c | 18 +++++++- filters/xz/xzfile.c | 4 -- plugins/example2/example2.c | 4 -- plugins/file/file.c | 4 -- plugins/streaming/streaming.c | 4 -- server/connections.c | 1 + server/quit.c | 5 ++- server/sockets.c | 7 ++-- server/test-utils.c | 79 +++++++...

...10 support SOCK_CLOEXEC, for example), and we're doing > ourselves a disservice by using silent fallback instead of actively > detecting with compile failure on systems that are still behind. > > [1] http://austingroupbugs.net/view.php?id=411 > > Conflicts: > filters/xz/xzfile.c - The fallback moved from plugins/xz/xzfile.c (and > in fact has been dead code since commit c879d310 made it a filter) > plugins/file/file.c - context changes in the meantime > src/internal.h - Moved to server/internal.h > --- > server/internal.h | 8 -------- >...

...sponds to > Ctrl+C? It prevents the command line from being used for a number of > hours if the contents of the workspace are large. This is ultimately caused by serialize() being non-interruptible. A relatively simple way to hang an R session for a long-ish time would therefore be: f <- xzfile(nullfile(), 'a+b') x <- rep(0, 1e9) # approx. 8 gigabytes, adjust for your RAM size serialize(x, f) close(f) This means that calling R_CheckUserInterrupt() between saving individual objects is not enough: R also needs to check for interrupts while saving sufficiently long vectors. Sinc...

Hello, Could save.image() be redesigned so that it promptly responds to Ctrl+C? It prevents the command line from being used for a number of hours if the contents of the workspace are large. -------------------------------------- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

On Thu, May 29, 2014 at 10:39:49AM -0700, knokknok wrote: > Not clear to me if the following malloc is freed within lzma or if this is a leak... > https://github.com/libguestfs/nbdkit/blob/master/plugins/xz/xzfile.c#L454 Sorry for the late reply - we don't use github for problem tracking so no one was looking at this. In this function (xzfile_read_block) the 'data' pointer is returned to the caller, who must free it. The calling code is a bit complicated because it puts the 'data' poin...

...tion(fc) : closing '/dev/full' failed: No space left on device > fc=gzfile("/dev/full", "w"); write.csv("a", file=fc); (res=close(fc)) NULL Warning message: In close.connection(fc) : closing '/dev/full' failed: No space left on device > fc=xzfile("/dev/full", "w"); write.csv("a", file=fc); (res=close(fc)) NULL Warning message: In close.connection(fc) : closing '/dev/full' failed: No space left on device > fc=bzfile("/dev/full", "w"); write.csv("a", file=fc); (res=clo...

...53 ++++++---- server/connections.c | 2 +- server/filters.c | 70 +++++-------- server/plugins.c | 142 ++++++++++----------------- server/protocol-handshake-newstyle.c | 4 +- filters/retry/retry.c | 23 +++++ filters/xz/xzfile.c | 4 + tests/Makefile.am | 2 + tests/test-retry-size.sh | 101 +++++++++++++++++++ 10 files changed, 275 insertions(+), 192 deletions(-) create mode 100755 tests/test-retry-size.sh -- 2.21.0

The inst/doc directory of the DAAG package has 6 files coral551.spot, ... that are around 0.85 MB each. It would be useful to be able to zip then, but that as matters stand interferes with the use of the Sweave file that uses them to demonstrate input of expression array data that is in the "spot" format. They do not automatically get unzipped when required. I have checked that

...pace left on device >> > fc=gzfile("/dev/full", "w"); write.csv("a", file=fc); (res=close(fc)) >> NULL >> Warning message: >> In close.connection(fc) : >> closing '/dev/full' failed: No space left on device >> > fc=xzfile("/dev/full", "w"); write.csv("a", file=fc); (res=close(fc)) >> NULL >> Warning message: >> In close.connection(fc) : >> closing '/dev/full' failed: No space left on device >> > fc=bzfile("/dev/full", "w")...

...| 64 ++++++++++++ filters/cache/blk.c | 12 ++- filters/cow/blk.c | 12 ++- filters/log/log.c | 22 ++++- filters/rate/rate.c | 20 +++- filters/stats/stats.c | 21 +++- filters/xz/xzfile.c | 4 - plugins/curl/curl.c | 1 + plugins/data/data.c | 1 + plugins/example2/example2.c | 5 +- plugins/example3/example3.c | 1 + plugins/ext2/ext2.c | 1 + plugins/file/file.c...

...v/full' failed: No space left on device > > fc=gzfile("/dev/full", "w"); write.csv("a", file=fc); (res=close(fc)) > NULL > Warning message: > In close.connection(fc) : > closing '/dev/full' failed: No space left on device > > fc=xzfile("/dev/full", "w"); write.csv("a", file=fc); (res=close(fc)) > NULL > Warning message: > In close.connection(fc) : > closing '/dev/full' failed: No space left on device > > fc=bzfile("/dev/full", "w"); write.csv("a&...

...zero = tar_zero, + .extents = tar_extents, + .cache = tar_cache, }; NBDKIT_REGISTER_FILTER(filter) diff --git a/filters/xz/xz.c b/filters/xz/xz.c index 26cfa959..2aa8c893 100644 --- a/filters/xz/xz.c +++ b/filters/xz/xz.c @@ -47,6 +47,7 @@ #include "xzfile.h" #include "blkcache.h" +#include "cleanup.h" static uint64_t maxblock = 512 * 1024 * 1024; static uint32_t maxdepth = 8; @@ -156,6 +157,21 @@ xz_prepare (struct nbdkit_next_ops *next_ops, void *nxdata, void *handle, return 0; } +/* Description. */ +static const c...

...tar_extents, > + .cache = tar_cache, > }; > > NBDKIT_REGISTER_FILTER(filter) > diff --git a/filters/xz/xz.c b/filters/xz/xz.c > index 26cfa959..2aa8c893 100644 > --- a/filters/xz/xz.c > +++ b/filters/xz/xz.c > @@ -47,6 +47,7 @@ > > #include "xzfile.h" > #include "blkcache.h" > +#include "cleanup.h" > > static uint64_t maxblock = 512 * 1024 * 1024; > static uint32_t maxdepth = 8; > @@ -156,6 +157,21 @@ xz_prepare (struct nbdkit_next_ops *next_ops, void *nxdata, void *handle, > return 0; >...

Duncan Murdoch has written at Thu, 6 Jul 2017 13:58:10 -0400 > On 06/07/2017 5:21 AM, Serguei Sokol wrote: >> I propose the following patch against the current >> R-devel/src/main/connection.c (cf. attached file). >> It gives (on my linux box): >> > fc=file("/dev/full", "w") >> > write.csv("a", file=fc) >> Error in

Applies on top of my pending series for the exportname filter, addressing one of the todo's in that cover letter. Eric Blake (2): filters: Add .export_description wrappers ext2: Supply .list_exports and .default_export filters/ext2/nbdkit-ext2-filter.pod | 3 +- tests/Makefile.am | 16 +++- filters/ext2/ext2.c | 125 +++++++++++++++++++---------