What Are lncRNAs?

lncRNAs are RNA transcripts longer than 200 nucleotides that do not code for proteins. Despite their non-coding nature, they play diverse roles in gene regulation, including chromatin remodeling, transcriptional control, and post-transcriptional processing. Unlike messenger RNAs (mRNAs), lncRNAs often function as scaffolds, decoys, or guides in cellular machinery, influencing biological processes such as cell differentiation, immune response, and even cancer metastasis.

Challenges in lncRNA Research

Identifying and understanding lncRNAs pose unique challenges:

1. High Sequence Variability: Unlike protein-coding genes, lncRNAs exhibit low sequence conservation across species, making functional predictions difficult.
2. Low Expression Levels: lncRNAs are often expressed at low levels, complicating their detection in transcriptomic data.
3. Diverse Functions: The multifunctional nature of lncRNAs requires advanced computational tools to decipher their roles in complex networks.

Bioinformatics: A Crucial Ally in lncRNA Research

Bioinformatics bridges the gap between raw biological data and meaningful insights, making it indispensable in lncRNA research. Here’s how:

1. Identification and Annotation

High-throughput sequencing technologies like RNA-seq generate vast amounts of data. Bioinformatics tools such as StringTie, Cufflinks, and HISAT2 help assemble and annotate lncRNAs from this data. Additionally, databases like NONCODE, LNCipedia, and Ensembl provide curated repositories of lncRNA sequences and annotations.

2. Functional Prediction

Bioinformatics algorithms predict the potential functions of lncRNAs by analyzing their interactions with DNA, RNA, and proteins. Tools like LncRNA2Function and RIblast utilize sequence motifs and secondary structure predictions to hypothesize about the roles of specific lncRNAs.

3. Network Construction

lncRNAs often act as regulatory hubs. Bioinformatics platforms such as Cytoscape enable the visualization of lncRNA-mediated networks, elucidating their roles in pathways like cell cycle regulation and apoptosis.

4. Epigenetic Studies

lncRNAs are known to interact with chromatin-modifying complexes, influencing gene expression epigenetically. Tools like ChIP-seq and ATAC-seq, combined with computational pipelines, identify these interactions and map them to the genome.

5. Clinical Applications

Bioinformatics aids in the discovery of lncRNA biomarkers for diseases like cancer and neurodegenerative disorders. Machine learning models analyze differential expression profiles, helping prioritize lncRNAs with therapeutic potential.

Case Study: lncRNAs in Cancer Research

lncRNAs such as HOTAIR and MALAT1 have been implicated in cancer progression. Bioinformatics analyses have revealed their roles in promoting metastasis and altering the tumor microenvironment. For example, transcriptome analysis in cancer patients identifies lncRNA expression signatures, enabling precision medicine approaches.

Future Directions

The fusion of bioinformatics with experimental biology is unlocking the secrets of lncRNAs. Advances in artificial intelligence, single-cell sequencing, and structural modeling promise to overcome current limitations. Here are some promising directions:

• Integrative Analysis: Combining multi-omics data to understand the interplay of lncRNAs with other biomolecules.
• CRISPR Screens: Leveraging bioinformatics to design CRISPR-based functional screens for lncRNAs.
• Therapeutic Development: Using bioinformatics to design lncRNA-based therapeutics, including antisense oligonucleotides and RNA interference tools.

Conclusion

lncRNAs are the hidden gems of the genome, and bioinformatics is the key to unearthing their full potential. As research progresses, lncRNAs could pave the way for novel diagnostics, targeted therapies, and personalized medicine, revolutionizing our approach to complex diseases.

The journey into the world of lncRNAs is only beginning, and bioinformatics will continue to play a pivotal role in decoding these molecular mysteries. Whether you’re a researcher, clinician, or bioinformatics enthusiast, the study of lncRNAs offers a fascinating frontier of discovery.

The Power of Evo 2: AI Meets DNA

Evo 2 is the largest AI model for biology ever created, trained on an astonishing 9.3 trillion DNA "letters" (nucleotides) carefully selected from genomes spanning the entire tree of life. This massive dataset ensures that Evo 2 can recognize patterns and relationships in genetic sequences at an unparalleled scale.

For the first time, scientists can design DNA with AI, moving beyond simple sequence analysis to active DNA generation. Evo 2 enables researchers to predict, modify, and even create entire genetic sequences, opening new possibilities in medicine, agriculture, and synthetic biology.

Decoding the Dark Genome

One of the biggest challenges in genetics is understanding the non-coding regions of DNA—vast stretches of the genome that do not code for proteins but play crucial roles in regulating gene expression. These regions control when and how genes are activated, influencing everything from development to disease.

Evo 2 is designed to decode these non-coding elements, helping researchers uncover their functions and use this knowledge to develop gene-based therapies, synthetic life forms, and precision agriculture solutions.

From Reading DNA to Writing It

To put Evo 2’s impact into perspective:

• Previous AI models could "read" DNA like a book, analyzing genetic sequences and identifying patterns.
• Evo 2 can "write" entirely new DNA, designing functional genes, chromosomes, and even full genomes from scratch.

This means scientists can now engineer biological systems with AI, designing new proteins, metabolic pathways, and genetic circuits to address real-world challenges.

A Step Toward Generative Biology

The Arc Institute describes Evo 2 as a major step toward "generative biology"—a revolutionary approach where AI is used to create novel biological structures rather than just analyzing existing ones. This could lead to breakthroughs such as:

• New medicines: AI-generated enzymes and proteins tailored for targeted therapies.
• Disease-resistant crops: Genetically optimized plants for higher yield and climate resilience.
• Synthetic organisms: Custom-designed microbes for bioremediation, biofuel production, and industrial applications.

An Open-Source Revolution

Unlike many proprietary AI models, Evo 2 is open source, making its capabilities accessible to researchers worldwide. This democratization of AI-driven biology means that scientists from different disciplines can collaborate, experiment, and innovate, accelerating discoveries in genetic engineering and synthetic biology.

With Evo 2, the boundaries of what’s possible in DNA design, genetic engineering, and biological innovation are being redrawn. The future of life sciences is no longer just about understanding life’s code—it’s about writing it.

That is the challenge researchers face when studying how bacteria adapt to different environments. A bacterial gene may appear to be linked to a particular habitat, when the real reason is simply that closely related bacteria happen to live there.

In their 2025 Genome Biology paper, Bujdoš, Walter, and O’Toole introduce aurora, a machine-learning tool designed to tackle this problem.

Aurora identifies potentially mislabeled or unusual bacterial strains before performing genome-wide association studies (GWAS). By cleaning up the dataset and accounting for bacterial evolutionary relationships, it can help researchers find genetic features that are more genuinely connected to habitat adaptation.

The researchers tested aurora using simulated and real bacterial datasets and found that it could recover important genetic associations even when datasets contained misleading labels.

The bigger lesson is simple: better biological discoveries often begin with better data.

Aurora gives researchers a new way to separate real genetic clues from misleading ones—and could help us better understand how bacteria adapt, survive, and evolve in the environments they call home.

Based on Bujdoš et al., “aurora: a machine learning GWAS tool for analyzing microbial habitat adaptation,” Genome Biology (2025).[Read the original paper](https://link.springer.com/article/10.1186/s13059-025-03524-7?)

Research Directions

Stony corals: evolution of novelty and photosymbiosis

Symbiotic acoels: cell type evolution and photosymbiosis

Animal genomes: structural evolution and gene regulation

https://sgel.biodiv.tw/home

A recent study published in Genome Biology (https://link.springer.com/article/10.1186/s13059-026-04280-y) addressed this challenge by introducing dicast (https://github.com/burgshrimps/dicast), a machine-learning approach for detecting structural variants in short-read sequencing data. Structural variants, such as large deletions, insertions, duplications, and inversions, can have significant biological and clinical implications, yet they are challenging to identify with short-read technologies. Because different detection methods frequently yield divergent results, researchers commonly employ consensus calling, considering a variant valid only if multiple tools detect it. While this approach reduces false positives, it relies on the potentially flawed assumption that the majority is always correct.

The researchers explored the impact of evaluating the supporting evidence for each variant, rather than simply tallying the number of algorithms that identified it. To establish a ground truth, they analyzed nine genomes using multiple sequencing technologies and 15 detection methods, initially identifying approximately 35 million potential variants. Through extensive filtering, evidence integration, and manual review of over 11,500 variants, they developed a robust benchmark comprising more than 236,000 structural variants. The findings underscored the complexity of the problem: short-read methods detected fewer than half of deletions and less than 10 percent of insertions, with performance declining markedly in repetitive genomic regions. In contrast, long-read technologies demonstrated superior detection capabilities. However, replacing the substantial volume of existing short-read data in clinical and research settings is not immediately feasible. Consequently, the researchers questioned whether short-read data might harbor more information than conventional analytical pipelines currently extract.

This line of inquiry led to the development of dicast. Rather than merely confirming agreement among multiple tools, dicast identifies patterns in sequencing data, including split and clipped reads, discordant read pairs, alignment characteristics, and the surrounding genomic context. An XGBoost machine-learning model evaluates which combinations of these signals are indicative of genuine structural variants. Thus, the approach shifts from tallying algorithmic consensus to interpreting the underlying evidence.

The researchers subsequently conducted a targeted evaluation by examining structural variants detected by only a single short-read tool, which are typically missed by consensus-based approaches. dicast successfully recovered approximately 81% of these single-caller deletions, insertions, and duplications. The signals for these variants were present in the data, but conventional filtering methods failed to integrate them effectively.

The utility of dicast was further demonstrated in cohorts with rare diseases, including congenital limb malformations, atrial fibrillation, and neuromuscular disorders. In one instance, dicast achieved a deletion recall rate of approximately 0.96, compared to 0.74 using consensus calling. The median number of variants requiring manual review was 29 per sample. Among 31 experimentally validated variants that standard filters would have missed, dicast identified 12, whereas consensus calling detected only one.

Overall, dicast identified approximately 20 percent more potential disease-causing deletions than consensus-based methods. While a 20 percent increase may appear modest, in clinical genomics such improvements can have significant practical implications. Missing a deletion may leave a case unresolved, whereas detecting a structural variant can provide critical diagnostic insights.

The study does not claim that machine learning has rendered short-read sequencing superior to long-read approaches. Instead, the results underscore the effectiveness of long-read sequencing for structural variant detection. However, dicast highlights a more nuanced perspective: substantial biological information may still be recoverable from the extensive short-read datasets already available.

The principal lesson extends beyond the detection of structural variants. For many years, bioinformatics pipelines have relied on threshold-based criteria, such as minimum coverage, quality scores, or support from multiple tools. While these rules are useful, biological phenomena do not always conform to rigid checklists; multiple weak signals, when considered collectively, can provide compelling evidence.

This perspective prompts consideration of the solitary variant: one algorithm identifies it, while several others do not. Traditional consensus techniques might have dismissed it, yet machine learning approaches evaluate the available evidence to determine whether the variant is plausible.

Occasionally, the most significant variant within a genome is the one that is almost universally overlooked.

Read more at https://link.springer.com/article/10.1186/s13059-026-04280-y

More about the basic perl module installation steps check this http://bioinformaticsonline.com/blog/view/710/how-to-install-perl-modules-manually-using-cpan-command-and-other-quick-ways

installing Bio::SCF perl module is daunting task, specieally because of it dependencies. Here is the steps, you need to follow to sucessfully install Bio::SCF module

#sudo apt-get install libbio-scf-perl #trev for visualization of scf file

1. You will need the zlib library which can be found at http://www.zlib.net/.

install zlib library first:

jitendra@jitendra-UNLOCK-INSTALL[zlib-1.2.11] ./configure []
Checking for gcc...
Checking for shared library support...
Building shared library libz.so.1.2.11 with gcc.
Checking for size_t... Yes.
Checking for off64_t... Yes.
Checking for fseeko... Yes.
Checking for strerror... Yes.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for attribute(visibility) support... Yes.
jitendra@jitendra-UNLOCK-INSTALL[zlib-1.2.11] make []
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o example.o test/example.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o adler32.o adler32.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o crc32.o crc32.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o deflate.o deflate.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o infback.o infback.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inffast.o inffast.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inflate.o inflate.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o trees.o trees.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o zutil.o zutil.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o compress.o compress.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzread.o gzread.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example example.o -L. libz.a
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o minigzip.o test/minigzip.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c
gcc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o libz.so.1.2.11 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo gzlib.lo gzread.lo gzwrite.lo -lc
rm -f libz.so libz.so.1
ln -s libz.so.1.2.11 libz.so
ln -s libz.so.1.2.11 libz.so.1
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o examplesh example.o -L. libz.so.1.2.11
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzipsh minigzip.o -L. libz.so.1.2.11
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o example64.o test/example.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example64 example64.o -L. libz.a
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o minigzip64.o test/minigzip.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L. libz.a
jitendra@jitendra-UNLOCK-INSTALL[zlib-1.2.11] sudo make install []
[sudo] password for jitendra:
rm -f /usr/local/lib/libz.a
cp libz.a /usr/local/lib
chmod 644 /usr/local/lib/libz.a
cp libz.so.1.2.11 /usr/local/lib
chmod 755 /usr/local/lib/libz.so.1.2.11
rm -f /usr/local/share/man/man3/zlib.3
cp zlib.3 /usr/local/share/man/man3
chmod 644 /usr/local/share/man/man3/zlib.3
rm -f /usr/local/lib/pkgconfig/zlib.pc
cp zlib.pc /usr/local/lib/pkgconfig
chmod 644 /usr/local/lib/pkgconfig/zlib.pc
rm -f /usr/local/include/zlib.h /usr/local/include/zconf.h
cp zlib.h zconf.h /usr/local/include
chmod 644 /usr/local/include/zlib.h /usr/local/include/zconf.h
 

2. Now make io_lib-1.9

In order to install this perl extension you have to install io-lib version 1.9 or higher from the Staden library (staden.sourceforge.net). This can be downloaded from https://sourceforge.net/project/showfiles.php?group_id=100316&package_id=108243&release_id=340318 confirm that the package installed correctly look for a library named "libread".

jitendra@jitendra-UNLOCK-INSTALL[io_lib-1.9.0] export CFLAGS="-fPIC" && ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking for main in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... 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 fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for unistd.h... (cached) yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking whether byte ordering is bigendian... no
checking for short... yes
checking size of short... 2
checking for int... yes
checking size of int... 4
checking for long... yes
checking size of long... 8
checking for inline... inline
checking for mode_t... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for cos in -lm... yes
checking for strdup... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating read/Makefile
config.status: creating progs/Makefile
config.status: creating config.h
config.status: executing depfiles commands
jitendra@jitendra-UNLOCK-INSTALL[io_lib-1.9.0] make []
make all-recursive
make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
Making all in read
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT Read.o -MD -MP -MF ".deps/Read.Tpo" -c -o Read.o Read.c; \
then mv -f ".deps/Read.Tpo" ".deps/Read.Po"; else rm -f ".deps/Read.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_extras.o -MD -MP -MF ".deps/scf_extras.Tpo" -c -o scf_extras.o scf_extras.c; \
then mv -f ".deps/scf_extras.Tpo" ".deps/scf_extras.Po"; else rm -f ".deps/scf_extras.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT translate.o -MD -MP -MF ".deps/translate.Tpo" -c -o translate.o translate.c; \
then mv -f ".deps/translate.Tpo" ".deps/translate.Po"; else rm -f ".deps/translate.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT compression.o -MD -MP -MF ".deps/compression.Tpo" -c -o compression.o `test -f '../ztr/compression.c' || echo './'`../ztr/compression.c; \
then mv -f ".deps/compression.Tpo" ".deps/compression.Po"; else rm -f ".deps/compression.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT ztr.o -MD -MP -MF ".deps/ztr.Tpo" -c -o ztr.o `test -f '../ztr/ztr.c' || echo './'`../ztr/ztr.c; \
then mv -f ".deps/ztr.Tpo" ".deps/ztr.Po"; else rm -f ".deps/ztr.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT ztr_translate.o -MD -MP -MF ".deps/ztr_translate.Tpo" -c -o ztr_translate.o `test -f '../ztr/ztr_translate.c' || echo './'`../ztr/ztr_translate.c; \
then mv -f ".deps/ztr_translate.Tpo" ".deps/ztr_translate.Po"; else rm -f ".deps/ztr_translate.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT fpoint.o -MD -MP -MF ".deps/fpoint.Tpo" -c -o fpoint.o `test -f '../abi/fpoint.c' || echo './'`../abi/fpoint.c; \
then mv -f ".deps/fpoint.Tpo" ".deps/fpoint.Po"; else rm -f ".deps/fpoint.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOABI.o -MD -MP -MF ".deps/seqIOABI.Tpo" -c -o seqIOABI.o `test -f '../abi/seqIOABI.c' || echo './'`../abi/seqIOABI.c; \
then mv -f ".deps/seqIOABI.Tpo" ".deps/seqIOABI.Po"; else rm -f ".deps/seqIOABI.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOALF.o -MD -MP -MF ".deps/seqIOALF.Tpo" -c -o seqIOALF.o `test -f '../alf/seqIOALF.c' || echo './'`../alf/seqIOALF.c; \
then mv -f ".deps/seqIOALF.Tpo" ".deps/seqIOALF.Po"; else rm -f ".deps/seqIOALF.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT ctfCompress.o -MD -MP -MF ".deps/ctfCompress.Tpo" -c -o ctfCompress.o `test -f '../ctf/ctfCompress.c' || echo './'`../ctf/ctfCompress.c; \
then mv -f ".deps/ctfCompress.Tpo" ".deps/ctfCompress.Po"; else rm -f ".deps/ctfCompress.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOCTF.o -MD -MP -MF ".deps/seqIOCTF.Tpo" -c -o seqIOCTF.o `test -f '../ctf/seqIOCTF.c' || echo './'`../ctf/seqIOCTF.c; \
then mv -f ".deps/seqIOCTF.Tpo" ".deps/seqIOCTF.Po"; else rm -f ".deps/seqIOCTF.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT expFileIO.o -MD -MP -MF ".deps/expFileIO.Tpo" -c -o expFileIO.o `test -f '../exp_file/expFileIO.c' || echo './'`../exp_file/expFileIO.c; \
then mv -f ".deps/expFileIO.Tpo" ".deps/expFileIO.Po"; else rm -f ".deps/expFileIO.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT seqIOPlain.o -MD -MP -MF ".deps/seqIOPlain.Tpo" -c -o seqIOPlain.o `test -f '../plain/seqIOPlain.c' || echo './'`../plain/seqIOPlain.c; \
then mv -f ".deps/seqIOPlain.Tpo" ".deps/seqIOPlain.Po"; else rm -f ".deps/seqIOPlain.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT misc_scf.o -MD -MP -MF ".deps/misc_scf.Tpo" -c -o misc_scf.o `test -f '../scf/misc_scf.c' || echo './'`../scf/misc_scf.c; \
then mv -f ".deps/misc_scf.Tpo" ".deps/misc_scf.Po"; else rm -f ".deps/misc_scf.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT read_scf.o -MD -MP -MF ".deps/read_scf.Tpo" -c -o read_scf.o `test -f '../scf/read_scf.c' || echo './'`../scf/read_scf.c; \
then mv -f ".deps/read_scf.Tpo" ".deps/read_scf.Po"; else rm -f ".deps/read_scf.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT write_scf.o -MD -MP -MF ".deps/write_scf.Tpo" -c -o write_scf.o `test -f '../scf/write_scf.c' || echo './'`../scf/write_scf.c; \
then mv -f ".deps/write_scf.Tpo" ".deps/write_scf.Po"; else rm -f ".deps/write_scf.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT array.o -MD -MP -MF ".deps/array.Tpo" -c -o array.o `test -f '../utils/array.c' || echo './'`../utils/array.c; \
then mv -f ".deps/array.Tpo" ".deps/array.Po"; else rm -f ".deps/array.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT compress.o -MD -MP -MF ".deps/compress.Tpo" -c -o compress.o `test -f '../utils/compress.c' || echo './'`../utils/compress.c; \
then mv -f ".deps/compress.Tpo" ".deps/compress.Po"; else rm -f ".deps/compress.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT error.o -MD -MP -MF ".deps/error.Tpo" -c -o error.o `test -f '../utils/error.c' || echo './'`../utils/error.c; \
then mv -f ".deps/error.Tpo" ".deps/error.Po"; else rm -f ".deps/error.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT files.o -MD -MP -MF ".deps/files.Tpo" -c -o files.o `test -f '../utils/files.c' || echo './'`../utils/files.c; \
then mv -f ".deps/files.Tpo" ".deps/files.Po"; else rm -f ".deps/files.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT find.o -MD -MP -MF ".deps/find.Tpo" -c -o find.o `test -f '../utils/find.c' || echo './'`../utils/find.c; \
then mv -f ".deps/find.Tpo" ".deps/find.Po"; else rm -f ".deps/find.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT mach-io.o -MD -MP -MF ".deps/mach-io.Tpo" -c -o mach-io.o `test -f '../utils/mach-io.c' || echo './'`../utils/mach-io.c; \
then mv -f ".deps/mach-io.Tpo" ".deps/mach-io.Po"; else rm -f ".deps/mach-io.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT open_trace_file.o -MD -MP -MF ".deps/open_trace_file.Tpo" -c -o open_trace_file.o `test -f '../utils/open_trace_file.c' || echo './'`../utils/open_trace_file.c; \
then mv -f ".deps/open_trace_file.Tpo" ".deps/open_trace_file.Po"; else rm -f ".deps/open_trace_file.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT read_alloc.o -MD -MP -MF ".deps/read_alloc.Tpo" -c -o read_alloc.o `test -f '../utils/read_alloc.c' || echo './'`../utils/read_alloc.c; \
then mv -f ".deps/read_alloc.Tpo" ".deps/read_alloc.Po"; else rm -f ".deps/read_alloc.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT strings.o -MD -MP -MF ".deps/strings.Tpo" -c -o strings.o `test -f '../utils/strings.c' || echo './'`../utils/strings.c; \
then mv -f ".deps/strings.Tpo" ".deps/strings.Po"; else rm -f ".deps/strings.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT traceType.o -MD -MP -MF ".deps/traceType.Tpo" -c -o traceType.o `test -f '../utils/traceType.c' || echo './'`../utils/traceType.c; \
then mv -f ".deps/traceType.Tpo" ".deps/traceType.Po"; else rm -f ".deps/traceType.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT xalloc.o -MD -MP -MF ".deps/xalloc.Tpo" -c -o xalloc.o `test -f '../utils/xalloc.c' || echo './'`../utils/xalloc.c; \
then mv -f ".deps/xalloc.Tpo" ".deps/xalloc.Po"; else rm -f ".deps/xalloc.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT vlen.o -MD -MP -MF ".deps/vlen.Tpo" -c -o vlen.o `test -f '../utils/vlen.c' || echo './'`../utils/vlen.c; \
then mv -f ".deps/vlen.Tpo" ".deps/vlen.Po"; else rm -f ".deps/vlen.Tpo"; exit 1; fi
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT hash_table.o -MD -MP -MF ".deps/hash_table.Tpo" -c -o hash_table.o `test -f '../utils/hash_table.c' || echo './'`../utils/hash_table.c; \
then mv -f ".deps/hash_table.Tpo" ".deps/hash_table.Po"; else rm -f ".deps/hash_table.Tpo"; exit 1; fi
../utils/hash_table.c: In function ‘HashFileOpen’:
../utils/hash_table.c:920:21: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
sprintf(aname, "%.*s%s", cp-fname+1, fname, hf->archive);
^
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../include -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT mFILE.o -MD -MP -MF ".deps/mFILE.Tpo" -c -o mFILE.o `test -f '../utils/mFILE.c' || echo './'`../utils/mFILE.c; \
then mv -f ".deps/mFILE.Tpo" ".deps/mFILE.Po"; else rm -f ".deps/mFILE.Tpo"; exit 1; fi
rm -f libread.a
ar cru libread.a Read.o scf_extras.o translate.o compression.o ztr.o ztr_translate.o fpoint.o seqIOABI.o seqIOALF.o ctfCompress.o seqIOCTF.o expFileIO.o seqIOPlain.o misc_scf.o read_scf.o write_scf.o array.o compress.o error.o files.o find.o mach-io.o open_trace_file.o read_alloc.o strings.o traceType.o xalloc.o vlen.o hash_table.o mFILE.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libread.a
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
Making all in progs
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT convert_trace.o -MD -MP -MF ".deps/convert_trace.Tpo" -c -o convert_trace.o convert_trace.c; \
then mv -f ".deps/convert_trace.Tpo" ".deps/convert_trace.Po"; else rm -f ".deps/convert_trace.Tpo"; exit 1; fi
gcc -fPIC -o convert_trace convert_trace.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT makeSCF.o -MD -MP -MF ".deps/makeSCF.Tpo" -c -o makeSCF.o makeSCF.c; \
then mv -f ".deps/makeSCF.Tpo" ".deps/makeSCF.Po"; else rm -f ".deps/makeSCF.Tpo"; exit 1; fi
gcc -fPIC -o makeSCF makeSCF.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT extract_seq.o -MD -MP -MF ".deps/extract_seq.Tpo" -c -o extract_seq.o extract_seq.c; \
then mv -f ".deps/extract_seq.Tpo" ".deps/extract_seq.Po"; else rm -f ".deps/extract_seq.Tpo"; exit 1; fi
gcc -fPIC -o extract_seq extract_seq.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT index_tar.o -MD -MP -MF ".deps/index_tar.Tpo" -c -o index_tar.o index_tar.c; \
then mv -f ".deps/index_tar.Tpo" ".deps/index_tar.Po"; else rm -f ".deps/index_tar.Tpo"; exit 1; fi
gcc -fPIC -o index_tar index_tar.o
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_dump.o -MD -MP -MF ".deps/scf_dump.Tpo" -c -o scf_dump.o scf_dump.c; \
then mv -f ".deps/scf_dump.Tpo" ".deps/scf_dump.Po"; else rm -f ".deps/scf_dump.Tpo"; exit 1; fi
gcc -fPIC -o scf_dump scf_dump.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_info.o -MD -MP -MF ".deps/scf_info.Tpo" -c -o scf_info.o scf_info.c; \
then mv -f ".deps/scf_info.Tpo" ".deps/scf_info.Po"; else rm -f ".deps/scf_info.Tpo"; exit 1; fi
gcc -fPIC -o scf_info scf_info.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT scf_update.o -MD -MP -MF ".deps/scf_update.Tpo" -c -o scf_update.o scf_update.c; \
then mv -f ".deps/scf_update.Tpo" ".deps/scf_update.Po"; else rm -f ".deps/scf_update.Tpo"; exit 1; fi
gcc -fPIC -o scf_update scf_update.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT get_comment.o -MD -MP -MF ".deps/get_comment.Tpo" -c -o get_comment.o get_comment.c; \
then mv -f ".deps/get_comment.Tpo" ".deps/get_comment.Po"; else rm -f ".deps/get_comment.Tpo"; exit 1; fi
gcc -fPIC -o get_comment get_comment.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT hash_tar.o -MD -MP -MF ".deps/hash_tar.Tpo" -c -o hash_tar.o hash_tar.c; \
then mv -f ".deps/hash_tar.Tpo" ".deps/hash_tar.Po"; else rm -f ".deps/hash_tar.Tpo"; exit 1; fi
gcc -fPIC -o hash_tar hash_tar.o ../read/libread.a -lz -lm
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT hash_extract.o -MD -MP -MF ".deps/hash_extract.Tpo" -c -o hash_extract.o hash_extract.c; \
then mv -f ".deps/hash_extract.Tpo" ".deps/hash_extract.Po"; else rm -f ".deps/hash_extract.Tpo"; exit 1; fi
gcc -fPIC -o hash_extract hash_extract.o ../read/libread.a -lz -lm
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -I../read -I../alf -I../abi -I../ctf -I../ztr -I../plain -I../scf -I../exp_file -I../utils -I/usr/local/include -fPIC -MT trace_dump.o -MD -MP -MF ".deps/trace_dump.Tpo" -c -o trace_dump.o trace_dump.c; \
then mv -f ".deps/trace_dump.Tpo" ".deps/trace_dump.Po"; else rm -f ".deps/trace_dump.Tpo"; exit 1; fi
gcc -fPIC -o trace_dump trace_dump.o ../read/libread.a -lz -lm
../read/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'

jitendra@jitendra-UNLOCK-INSTALL[io_lib-1.9.0] sudo make install []
[sudo] password for jitendra:
Making install in read
make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
test -z "/usr/local/lib" || mkdir -p -- "/usr/local/lib"
/usr/bin/install -c -m 644 'libread.a' '/usr/local/lib/libread.a'
ranlib '/usr/local/lib/libread.a'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/read'
Making install in progs
make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
test -z "/usr/local/bin" || mkdir -p -- "/usr/local/bin"
/usr/bin/install -c 'convert_trace' '/usr/local/bin/convert_trace'
/usr/bin/install -c 'makeSCF' '/usr/local/bin/makeSCF'
/usr/bin/install -c 'extract_seq' '/usr/local/bin/extract_seq'
/usr/bin/install -c 'index_tar' '/usr/local/bin/index_tar'
/usr/bin/install -c 'scf_dump' '/usr/local/bin/scf_dump'
/usr/bin/install -c 'scf_info' '/usr/local/bin/scf_info'
/usr/bin/install -c 'scf_update' '/usr/local/bin/scf_update'
/usr/bin/install -c 'get_comment' '/usr/local/bin/get_comment'
/usr/bin/install -c 'hash_tar' '/usr/local/bin/hash_tar'
/usr/bin/install -c 'hash_extract' '/usr/local/bin/hash_extract'
/usr/bin/install -c 'trace_dump' '/usr/local/bin/trace_dump'
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0/progs'
make[1]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[2]: Entering directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[2]: Nothing to be done for 'install-exec-am'.
test -z "/usr/local/man/man3" || mkdir -p -- "/usr/local/man/man3"
/usr/bin/install -c -m 644 './man/man3/exp2read.3' '/usr/local/man/man3/exp2read.3'
/usr/bin/install -c -m 644 './man/man3/ExperimentFile.3' '/usr/local/man/man3/ExperimentFile.3'
/usr/bin/install -c -m 644 './man/man3/fread_reading.3' '/usr/local/man/man3/fread_reading.3'
/usr/bin/install -c -m 644 './man/man3/fread_scf.3' '/usr/local/man/man3/fread_scf.3'
/usr/bin/install -c -m 644 './man/man3/fwrite_reading.3' '/usr/local/man/man3/fwrite_reading.3'
/usr/bin/install -c -m 644 './man/man3/fwrite_scf.3' '/usr/local/man/man3/fwrite_scf.3'
/usr/bin/install -c -m 644 './man/man3/read2exp.3' '/usr/local/man/man3/read2exp.3'
/usr/bin/install -c -m 644 './man/man3/read2scf.3' '/usr/local/man/man3/read2scf.3'
/usr/bin/install -c -m 644 './man/man3/read_allocate.3' '/usr/local/man/man3/read_allocate.3'
/usr/bin/install -c -m 644 './man/man3/read_deallocate.3' '/usr/local/man/man3/read_deallocate.3'
/usr/bin/install -c -m 644 './man/man3/read_reading.3' '/usr/local/man/man3/read_reading.3'
/usr/bin/install -c -m 644 './man/man3/read_scf.3' '/usr/local/man/man3/read_scf.3'
/usr/bin/install -c -m 644 './man/man3/read_scf_header.3' '/usr/local/man/man3/read_scf_header.3'
/usr/bin/install -c -m 644 './man/man3/scf2read.3' '/usr/local/man/man3/scf2read.3'
/usr/bin/install -c -m 644 './man/man3/write_reading.3' '/usr/local/man/man3/write_reading.3'
/usr/bin/install -c -m 644 './man/man3/write_scf.3' '/usr/local/man/man3/write_scf.3'
/usr/bin/install -c -m 644 './man/man3/write_scf_header.3' '/usr/local/man/man3/write_scf_header.3'
test -z "/usr/local/man/man4" || mkdir -p -- "/usr/local/man/man4"
/usr/bin/install -c -m 644 './man/man4/Read.4' '/usr/local/man/man4/Read.4'
test -z "/usr/local/include/io_lib" || mkdir -p -- "/usr/local/include/io_lib"
/usr/bin/install -c -m 644 'read/Read.h' '/usr/local/include/io_lib/Read.h'
/usr/bin/install -c -m 644 'read/scf_extras.h' '/usr/local/include/io_lib/scf_extras.h'
/usr/bin/install -c -m 644 'read/translate.h' '/usr/local/include/io_lib/translate.h'
/usr/bin/install -c -m 644 'abi/abi.h' '/usr/local/include/io_lib/abi.h'
/usr/bin/install -c -m 644 'abi/fpoint.h' '/usr/local/include/io_lib/fpoint.h'
/usr/bin/install -c -m 644 'abi/seqIOABI.h' '/usr/local/include/io_lib/seqIOABI.h'
/usr/bin/install -c -m 644 'alf/alf.h' '/usr/local/include/io_lib/alf.h'
/usr/bin/install -c -m 644 'ctf/seqIOCTF.h' '/usr/local/include/io_lib/seqIOCTF.h'
/usr/bin/install -c -m 644 'exp_file/expFileIO.h' '/usr/local/include/io_lib/expFileIO.h'
/usr/bin/install -c -m 644 'plain/plain.h' '/usr/local/include/io_lib/plain.h'
/usr/bin/install -c -m 644 'scf/scf.h' '/usr/local/include/io_lib/scf.h'
/usr/bin/install -c -m 644 'utils/array.h' '/usr/local/include/io_lib/array.h'
/usr/bin/install -c -m 644 'utils/compress.h' '/usr/local/include/io_lib/compress.h'
/usr/bin/install -c -m 644 'utils/error.h' '/usr/local/include/io_lib/error.h'
/usr/bin/install -c -m 644 'utils/mach-io.h' '/usr/local/include/io_lib/mach-io.h'
/usr/bin/install -c -m 644 'utils/misc.h' '/usr/local/include/io_lib/misc.h'
/usr/bin/install -c -m 644 'utils/open_trace_file.h' '/usr/local/include/io_lib/open_trace_file.h'
/usr/bin/install -c -m 644 'utils/tar_format.h' '/usr/local/include/io_lib/tar_format.h'
/usr/bin/install -c -m 644 'utils/traceType.h' '/usr/local/include/io_lib/traceType.h'
/usr/bin/install -c -m 644 'utils/xalloc.h' '/usr/local/include/io_lib/xalloc.h'
/usr/bin/install -c -m 644 'utils/mFILE.h' '/usr/local/include/io_lib/mFILE.h'
/usr/bin/install -c -m 644 'utils/stdio_hack.h' '/usr/local/include/io_lib/stdio_hack.h'
/usr/bin/install -c -m 644 'utils/vlen.h' '/usr/local/include/io_lib/vlen.h'
/usr/bin/install -c -m 644 'utils/hash_table.h' '/usr/local/include/io_lib/hash_table.h'
/usr/bin/install -c -m 644 'utils/os.h' '/usr/local/include/io_lib/os.h'
/usr/bin/install -c -m 644 'ztr/compression.h' '/usr/local/include/io_lib/compression.h'
/usr/bin/install -c -m 644 'ztr/ztr.h' '/usr/local/include/io_lib/ztr.h'
make[2]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'
make[1]: Leaving directory '/home/jitendra/Downloads/io_lib-1.9.0'

3. Now install Bio::SCF

Now follows these steps:

tar zxf Bio::SCF.tar
cd Bio::SCF
perl Makefile.PL
make
make test
make install

jitendra@jitendra-UNLOCK-INSTALL[Bio-SCF-1.01] perl Makefile.PL []
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::SCF
Writing MYMETA.yml and MYMETA.json
jitendra@jitendra-UNLOCK-INSTALL[Bio-SCF-1.01] make []
cp SCF.pm blib/lib/Bio/SCF.pm
cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm
Running Mkbootstrap for Bio::SCF ()
chmod 644 "SCF.bs"
"/usr/bin/perl" "/usr/share/perl/5.22/ExtUtils/xsubpp" -typemap "/usr/share/perl/5.22/ExtUtils/typemap" SCF.xs > SCF.xsc && mv SCF.xsc SCF.c
Please specify prototyping behavior for SCF.xs (see perlxs manual)
x86_64-linux-gnu-gcc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.01\" -DXS_VERSION=\"1.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.22/CORE" -DLITTLE_ENDIAN SCF.c
In file included from /usr/lib/x86_64-linux-gnu/perl/5.22/CORE/perl.h:5546:0,
from SCF.xs:5:
SCF.xs: In function ‘XS_Bio__SCF_get_scf_pointer’:
SCF.xs:57:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
ret_val = newSViv((int)scf_data);
^
/usr/lib/x86_64-linux-gnu/perl/5.22/CORE/embed.h:402:40: note: in definition of macro ‘newSViv’
#define newSViv(a) Perl_newSViv(aTHX_ a)
^
SCF.xs: In function ‘XS_Bio__SCF_get_scf_fpointer’:
SCF.xs:80:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
ret_val = newSViv((int)scf_data);
^
/usr/lib/x86_64-linux-gnu/perl/5.22/CORE/embed.h:402:40: note: in definition of macro ‘newSViv’
#define newSViv(a) Perl_newSViv(aTHX_ a)
^
SCF.xs: In function ‘XS_Bio__SCF_scf_free’:
SCF.xs:89:17: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
scf_deallocate((Scf *)scf_pointer);
^
SCF.xs: In function ‘XS_Bio__SCF_get_comments’:
SCF.xs:95:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_set_comments’:
SCF.xs:108:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_scf_write’:
SCF.xs:121:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_scf_fwrite’:
SCF.xs:137:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_get_from_header’:
SCF.xs:159:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_get_at’:
SCF.xs:186:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_set_base_at’:
SCF.xs:242:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
SCF.xs: In function ‘XS_Bio__SCF_set_at’:
SCF.xs:255:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
Scf *scf_data = (Scf *)scf_pointer;
^
rm -f blib/arch/auto/Bio/SCF/SCF.so
x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \
-lread -lz \

/usr/local/lib/libread.a(open_trace_file.o): In function `find_file_url':
open_trace_file.c:(.text+0xaf4): warning: the use of `tempnam' is dangerous, better use `mkstemp'
chmod 755 blib/arch/auto/Bio/SCF/SCF.so
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SCF.bs blib/arch/auto/Bio/SCF/SCF.bs 644
Manifying 1 pod document

jitendra@jitendra-Aspire-S3-391[parallelLastz] sudo cpan install abs  [ 4:43AM]
Going to read '/home/jitendra/.cpan/Metadata'
  Database was generated on Thu, 02 May 2019 00:08:06 GMT
Don't be silly, you can't install David Brownlee ;-)

sort a space-delimited file based on its first column, then the second if the first is the same, and so on:
sort input.txt

sort a huge file (GNU sort ONLY):
sort -S 1500M -t $HOME/tmp input.txt > sorted.txt

sort starting from the third column, skipping the first two columns:
sort +2 input.txt

sort the second column as numbers, descending order; if identical, sort the 3rd as strings, ascending order:
sort -k2,2nr -k3,3 input.txt

sort starting from the 4th character at column 2, as numbers:
sort -k2.4n input.txt

More Linxu sort command information

If you have any sort commands you'd like to share, please add them to our comments section below. For more help, you can also type:

man sort

or

sort --help

on your Unix/Linux system.

Additional Information:

If you have any questions about scientific aspects of this position, please contact Prof. Lars Bertram, head of LIGA (lars.bertram@uni-luebeck.de).

Please contact Ms. Anna Wolbert for further questions about administrative details (recruiting@uksh.de).

Weitere Informationen erhalten Sie auch unter www.uksh.de/karriere.

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