I am getting below error where its actually giving out of disk. This is because of allocated space for srt file generation is not enough. so we decided to change the path with huge space..Is it possible to change it through program?
SYSTEM ERROR: I/O error 0 in writeto, ret 2048, file 56(/mfgtmp/tmp/srtE5yybD), addr 77010944. (290)
The -T startup parameter defines the folder for temporary files like srt files.
https://docs.progress.com/bundle/openedge-abl-manage-applications-117/page/Distributing-temporary-files.html
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Is there a more efficient way than
int fileSize = size(readFileLines(fileLoc));
to get the total number of lines in a file? I presume this code has to read the entire file first, which could become costly for huge files.
I have looked into IO and Loc whether some of this info might be saved in conjunction with the file.
This is the way, unless you'd like to call wc -l via util::ShellExec 😁
Apart from streaming the file and saving some memory counting lines is always linear in the size of the file so you won't win much time.
I have been obtaining .zip archives of genome annotation from NCBI (mainly gff files). In order save disk space I prefer not to unzip the archive, but to read these files directly into R using unz(). However, it seems that unz() is unable to extract files from the end of 'large' zip files:
ncbi.zip <- "file_location/name.zip"
files <- unzip(ncbi.zip, list=TRUE)
gff.files <- files$Name[ grep("gff$", files$Name) ]
## this works
gff.128 <- readLines( unz(ncbi.zip, gff.files[128]) )
## this gives an empty data structure (read.table() stops
## with an error saying no lines or similar
gff.129 <- readLines( unz(ncbi.zip, gff.files[129]) )
## there are 31 more gff files after the 129th one.
## no lines are read from any of these.
The zip file itself seems to be fine; I can unzip the specific files using unzip on the command line and unzip -t does not report any errors.
I've tried this with R versions 3.5 (openSuse Leap 15.1), 3.6, and 4.2 (centOS 7) and with more than one zip file and get exactly the same result.
I attached strace to R whilst reading in the 128 and 129th file. In both cases I get a lot of lseek towards the end of file (offset 2845892608, larger than 2^31) to start with. This is where I assume the zip directory can be found. For the 128th file (the one that can be read), I eventually get an lseek to an offset slightly below 2^31, followed by a set of lseeks and reads (that extend beyone 2^31).
For the 129th file, I get the same reads towards the end of the file, but then rather than finding a position within the file I get:
lseek(3, 2845933568, SEEK_SET) = 2845933568
lseek(3, 4294963200, SEEK_SET) = 4294963200
read(3, "", 4096) = 0
lseek(3, 4095, SEEK_CUR) = 4294967295
read(3, "", 4096) = 0
Which is a bit weird since the file itself is only about 2.8 GB. 4294967295, is of course 2^32 - 1.
To me this feels like an integer overflow bug, and I am considering to post a bug report. But am wondering if anyone has seen something similar before or if I am doing something stupid.
Having done what I should have started with (reading the specification for the zip64 format specification), it's actually clear that this is not an integer overflow error.
Zip files contain a central directory at the end of the archive; this contains amongst other things the names of the compressed files and the offset of the compressed data in the zip archive. The offset (and file size fields) are only given 4 bytes each in the standard directory field; when the offset is larger than this it should instead be given in the extra fields section and the value in the standard field should be set to 0xFFFFFFFF. Since this is the offset that gets used when reading the file it seems clear that the problem lies in the parsing of the extra field.
I had a look at the source code for R 4.2.1 and it seems that the problem is due to the way the offset specified in the standard offset field is tested:
if(file_info.uncompressed_size == (ZPOS64_T)(unsigned long)-1)
changing this == 0xFFFFFFFF seems to fix the problem.
I've submitted a bug report to R. Hopefully changing the check will not have any unintended consequences and the issue will be fixed.
Still, I'm curious as to whether anyone else has come across the same issue. Seems a bit unlikely that my experience is unique.
I wrote a script that executes commands in parallel. I let them all write an entry to the same log file. It does not matter if the order is wrong or entries are interleaved, but i noticed that some entries are missing. I should probably lock the file before writing, however, is it true that if multiple processes try to write to a file simultaneously, it will result in missing entries?
Yes, if different processes independently open and write to the same file, it may result in overlapping writes and missing data. This happens because each process will get its own file pointer, that advances only by local writes.
Instead of locking, a better option might be to open the log file once in an ancestor of all worker processes, have it inherited across fork(), and used by them for logging. This means that there will be a single shared file pointer, that advances when any of the processes writes a new entry.
In a script you should use ">> file" (double greater than) to append output to that file. The interpreter will open the destination in "append" mode. If your program also wants to append, follow the directives below:
Open a text file in "append" mode ("a+") and give preference to printing only full lines (don't do multiple 'print' followed by a final 'println', but print the entire line with a single 'println').
The fopen documentation states this:
DESCRIPTION
The fopen() function opens the file whose pathname is the
string pointed to by filename, and associates a stream with
it.
The argument mode points to a string beginning with one of
the following sequences:
r or rb Open file for reading.
w or wb Truncate to zero length or create file
for writing.
a or ab Append; open or create file for writing
at end-of-file.
r+ or rb+ or r+b Open file for update (reading and writ-
ing).
w+ or wb+ or w+b Truncate to zero length or create file
for update.
a+ or ab+ or a+b Append; open or create file for update,
writing at end-of-file.
The character b has no effect, but is allowed for ISO C
standard conformance (see standards(5)). Opening a file with
read mode (r as the first character in the mode argument)
fails if the file does not exist or cannot be read.
Opening a file with append mode (a as the first character in
the mode argument) causes all subsequent writes to the file
to be forced to the then current end-of-file, regardless of
intervening calls to fseek(3C). If two separate processes
open the same file for append, each process may write freely
to the file without fear of destroying output being written
by the other. The output from the two processes will be
intermixed in the file in the order in which it is written.
It is because of this intermixing that you want to give preference to
using only 'println' (or its equivalent).
I want to open a file for write and I have been given the file descriptor for that file.
I know that fdopen can be used to write to the file as follows:
FILE * fp;
fp = fdopen(filedes, "a+");
fwrite("\n", sizeof(char), 1, fp);
Is there any other way to achive the same, i.e., write to a file given a file descriptor?
Thanks
Is there any other way to achive the same, i.e., write to a file given
a file descriptor
You can write directly using the system call write(2).
write(fd, "\n", 1);
You can write a buffer of data to a file descriptor with the write system call.
I'm building a SWF using the command line compiler mxmlc.exe. The compiler writes the output file size as part of it's stdout. If I run the compiler multiple times in succession without changing the actual source code, I see the file size bounce up and down a few bytes at a time.
C:\>mxmlc.exe Gallery.as
C:\Gallery.swf (28443 bytes)
C:\>mxmlc.exe Gallery.as
C:\Gallery.swf (28442 bytes)
C:\>mxmlc.exe Gallery.as
C:\Gallery.swf (28440 bytes)
C:\>mxmlc.exe Gallery.as
C:\Gallery.swf (28442 bytes)
I can't think why this would possibly be the case. Even if I delete the output file each time, the re-generated file size still varies in this way.
Any ideas why?
The Flex compiler includes some information in your SWF that changes from build-to-build, such as the date and time it was built. The SWF is then compressed. Sometimes the compression will work a bit better than others for the varying metadata, thus the minor changes in file size.
http://livedocs.adobe.com/flex/3/html/help.html?content=compilers_16.html#145380