read.bam.tags cannot identify reads strand

[Bumblebee5k8m7]

I'm using CentOs 7 with gcc version 8.3.0 to install spp version 1.6 package. Even though the packages was installed, it reported some warnings. The installation code is shown below
`Warning in untar2(tarfile, files, list, exdir, restore_times) :
skipping pax global extended headers

• installing to library ‘/home/hyu/R/lib64/R/library’
• installing source package ‘spp’ ...
  checking for gcc... gcc
  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 gcc accepts -g... yes
  checking for gcc option to accept ISO C89... none needed
  checking for BZ2_bzDecompressInit in -lbz2... yes
  checking for g++... g++
  checking whether we are using the GNU C++ compiler... yes
  checking whether g++ accepts -g... yes
  checking for grep that handles long lines and -e... /usr/bin/grep
  checking how to run the C++ preprocessor... g++ -E
  checking for a sed that does not truncate output... /usr/bin/sed
  checking for Boost headers version >= 1.41.0... yes
  checking for Boost's header version... 1_53
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -std=c++11 -fpic -g -O2 -c bed2vector.cpp -o bed2vector.o
  gcc -std=gnu99 -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c cdensum.c -o cdensum.o
  cdensum.c:7:14: warning: extra tokens at end of #undef directive
  #undef DEBUG 1
  ^
  gcc -std=gnu99 -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c maqmap.c -o maqmap.o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -std=c++11 -fpic -g -O2 -c maqread.cpp -o maqread.o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -std=c++11 -fpic -g -O2 -c peaks.cpp -o peaks.o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -std=c++11 -fpic -g -O2 -c wdl.cpp -o wdl.o
  g++ -shared -L/home/hyu/R/lib64/R/lib -L/usr/local/lib64 -o spp.so bed2vector.o cdensum.o maqmap.o maqread.o peaks.o w dl.o -lbz2 -lz -L/home/hyu/R/lib64/R/lib -lR
  installing to /home/hyu/R/lib64/R/library/spp/libs
  ** R
  ** preparing package for lazy loading
  ** help
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/find.binding.positions.Rd:100: unknown macro '\item'
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/find.binding.positions.Rd:101: unknown macro '\item'
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/find.binding.positions.Rd:102: unknown macro '\item'
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/find.binding.positions.Rd:103: unknown macro '\item'
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/find.binding.positions.Rd:105: unknown macro '\item'
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/find.binding.positions.Rd:109: unknown macro '\item'
  Warning: bad markup (extra space?) at get.binding.characteristics.Rd:42:13
  Warning: bad markup (extra space?) at get.binding.characteristics.Rd:44:32
  Warning: bad markup (extra space?) at get.binding.characteristics.Rd:48:28
  Warning: bad markup (extra space?) at get.binding.characteristics.Rd:52:22
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:9: unknown macro '\item'
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:10: unknown macro '\item'
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:11: unknown macro '\item'
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:12: unknown macro '\item'
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:13: unknown macro '\item'
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:14: unknown macro '\item'
  Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:15: unknown macro '\item'
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
• DONE (spp)`

And then I use the read.bam.tags function to read a bam file. However, tags of the object from the function were all identify as positive strand. The results was showed below:

`

which(chip.data[["tags"]]$chr01 < 0)
integer(0)`

so how to solve the problem?

Best Regards!

Liquan

[fferrari]

The code in the warnings below shows you are using spp1.15 Please the latest 1.16 Also use the latest R version, not the default one in centos Il mar 12 nov 2019, 04:36 Bumblebee5k8m7 <notifications@github.com> ha scritto:

…

I'm using CentOs 7 with gcc version 8.3.0 to install spp version 1.6 package. Even though the packages was installed, it reported some warnings. The installation code is shown below `Warning in untar2(tarfile, files, list, exdir, restore_times) : skipping pax global extended headers - installing to library ‘/home/hyu/R/lib64/R/library’ - installing *source* package ‘spp’ ... checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for BZ2_bzDecompressInit in -lbz2... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for grep that handles long lines and -e... /usr/bin/grep checking how to run the C++ preprocessor... g++ -E checking for a sed that does not truncate output... /usr/bin/sed checking for Boost headers version >= 1.41.0... yes checking for Boost's header version... 1_53 configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -std=c++11 -fpic -g -O2 -c bed2vector.cpp -o bed2vector.o gcc -std=gnu99 -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c cdensum.c -o cdensum.o cdensum.c:7:14: warning: extra tokens at end of #undef directive #undef DEBUG 1 ^ gcc -std=gnu99 -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c maqmap.c -o maqmap.o g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -std=c++11 -fpic -g -O2 -c maqread.cpp -o maqread.o g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -std=c++11 -fpic -g -O2 -c peaks.cpp -o peaks.o g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -std=c++11 -fpic -g -O2 -c wdl.cpp -o wdl.o g++ -shared -L/home/hyu/R/lib64/R/lib -L/usr/local/lib64 -o spp.so bed2vector.o cdensum.o maqmap.o maqread.o peaks.o w dl.o -lbz2 -lz -L/home/hyu/R/lib64/R/lib -lR installing to /home/hyu/R/lib64/R/library/spp/libs ** R ** preparing package for lazy loading ** help Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/find.binding.positions.Rd 💯 unknown macro '\item' Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/find.binding.positions.Rd:101: unknown macro '\item' Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/find.binding.positions.Rd:102: unknown macro '\item' Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/find.binding.positions.Rd:103: unknown macro '\item' Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/find.binding.positions.Rd:105: unknown macro '\item' Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/find.binding.positions.Rd:109: unknown macro '\item' Warning: bad markup (extra space?) at get.binding.characteristics.Rd:42:13 Warning: bad markup (extra space?) at get.binding.characteristics.Rd:44:32 Warning: bad markup (extra space?) at get.binding.characteristics.Rd:48:28 Warning: bad markup (extra space?) at get.binding.characteristics.Rd:52:22 Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:9: unknown macro '\item' Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:10: unknown macro '\item' Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:11: unknown macro '\item' Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:12: unknown macro '\item' Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:13: unknown macro '\item' Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:14: unknown macro '\item' Warning: /tmp/RtmpZaUhQX/R.INSTALL81ee4f48b99d/spp-1.15.1/man/output.binding.results.Rd:15: unknown macro '\item' *** installing help indices ** building package indices ** testing if installed package can be loaded - DONE (spp)And then I use the read.bam.tags function to read a bam file. However, tags of the object from the function were all identify as positive strand. The results was showed below: which(chip.data[["tags"]]$chr01 < 0) integer(0)` so how to solve the problem? Best Regards! Liquan — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#37?email_source=notifications&email_token=ABJ7XWIYAICZYI3PUU3ZGO3QTIQDBA5CNFSM4JL5YLXKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HYSRGMA>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABJ7XWPY5IW7XLYJIBF3IWLQTIQDBANCNFSM4JL5YLXA> .

[Bumblebee5k8m7]

The code in the warnings below shows you are using spp1.15 Please the latest 1.16 Also use the latest R version, not the default one in centos Il mar 12 nov 2019, 04:36 Bumblebee5k8m7 notifications@github.com ha scritto:

Before installation I have read the dependencies:
Package: spp
Type: Package
Title: ChIP-Seq Processing Pipeline
Version: 1.15.5
Author: Peter K
Date: 2018-07-19
Depends: R (>= 3.3.0), Rcpp

It seems that errors should not happen while I'm using R version 3.3.1. Besides upgrading R is not very convenient. So can you point out the problems behind the issue? Then I'm going to fix it.

[fferrari]

Please try the latest spp version 1.16 Il mar 12 nov 2019, 12:18 Bumblebee5k8m7 <notifications@github.com> ha scritto:

…

The code in the warnings below shows you are using spp1.15 Please the latest 1.16 Also use the latest R version, not the default one in centos Il mar 12 nov 2019, 04:36 Bumblebee5k8m7 ***@***.*** ha scritto: Before installation I have read the dependencies: Package: spp Type: Package Title: ChIP-Seq Processing Pipeline Version: 1.15.5 Author: Peter K Date: 2018-07-19 Depends: R (>= 3.3.0), Rcpp It seems that errors should not happen while I'm using R version 3.3.1. Besides upgrading R is not very convenient. So can you point out the problems behind the issue? Then I'm going to fix it. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37?email_source=notifications&email_token=ABJ7XWOHXR57RFTIKWU6IPLQTKGIXA5CNFSM4JL5YLXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDZ5OUQ#issuecomment-552851282>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABJ7XWMICYZTGGW4GA2RS3LQTKGIXANCNFSM4JL5YLXA> .

[fferrari]

https://cran.r-project.org/web/packages/spp/index.html Il mar 12 nov 2019, 12:24 Francesco Ferrari < ferrari.francesco.nospam@gmail.com> ha scritto:

…

Please try the latest spp version 1.16 Il mar 12 nov 2019, 12:18 Bumblebee5k8m7 ***@***.***> ha scritto: > The code in the warnings below shows you are using spp1.15 Please the > latest 1.16 Also use the latest R version, not the default one in centos Il > mar 12 nov 2019, 04:36 Bumblebee5k8m7 ***@***.*** ha > scritto: > > Before installation I have read the dependencies: > Package: spp > Type: Package > Title: ChIP-Seq Processing Pipeline > Version: 1.15.5 > Author: Peter K > Date: 2018-07-19 > Depends: R (>= 3.3.0), Rcpp > > It seems that errors should not happen while I'm using R version 3.3.1. > Besides upgrading R is not very convenient. So can you point out the > problems behind the issue? Then I'm going to fix it. > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#37?email_source=notifications&email_token=ABJ7XWOHXR57RFTIKWU6IPLQTKGIXA5CNFSM4JL5YLXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDZ5OUQ#issuecomment-552851282>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ABJ7XWMICYZTGGW4GA2RS3LQTKGIXANCNFSM4JL5YLXA> > . >

[Bumblebee5k8m7]

https://cran.r-project.org/web/packages/spp/index.html Il mar 12 nov 2019, 12:24 Francesco Ferrari < ferrari.francesco.nospam@gmail.com> ha scritto:
…
Please try the latest spp version 1.16 Il mar 12 nov 2019, 12:18 Bumblebee5k8m7 @.> ha scritto: > The code in the warnings below shows you are using spp1.15 Please the > latest 1.16 Also use the latest R version, not the default one in centos Il > mar 12 nov 2019, 04:36 Bumblebee5k8m7 @. ha > scritto: > > Before installation I have read the dependencies: > Package: spp > Type: Package > Title: ChIP-Seq Processing Pipeline > Version: 1.15.5 > Author: Peter K > Date: 2018-07-19 > Depends: R (>= 3.3.0), Rcpp > > It seems that errors should not happen while I'm using R version 3.3.1. > Besides upgrading R is not very convenient. So can you point out the > problems behind the issue? Then I'm going to fix it. > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#37?email_source=notifications&email_token=ABJ7XWOHXR57RFTIKWU6IPLQTKGIXA5CNFSM4JL5YLXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDZ5OUQ#issuecomment-552851282>, > or unsubscribe > https://github.com/notifications/unsubscribe-auth/ABJ7XWMICYZTGGW4GA2RS3LQTKGIXANCNFSM4JL5YLXA > . >

I have tried and it seems the position are all on positive strand. Below is the result:
`

which(chip.data[["tags"]]$chr01 < 0)
integer(0)
packageVersion("spp")
[1] ‘1.16.0
’`

Thanks for your help

[fferrari]

Maybe a problem with the bsm file format? Can you show some lines from the bam file? Il mar 12 nov 2019, 12:42 Bumblebee5k8m7 <notifications@github.com> ha scritto:

…

https://cran.r-project.org/web/packages/spp/index.html Il mar 12 nov 2019, 12:24 Francesco Ferrari < ***@***.***> ha scritto: … <#m_7811761540078084699_> Please try the latest spp version 1.16 Il mar 12 nov 2019, 12:18 Bumblebee5k8m7 *@*.*> ha scritto: > The code in the warnings below shows you are using spp1.15 Please the > latest 1.16 Also use the latest R version, not the default one in centos Il > mar 12 nov 2019, 04:36 Bumblebee5k8m7 @.* ha > scritto: > > Before installation I have read the dependencies: > Package: spp > Type: Package > Title: ChIP-Seq Processing Pipeline > Version: 1.15.5 > Author: Peter K > Date: 2018-07-19 > Depends: R (>= 3.3.0), Rcpp > > It seems that errors should not happen while I'm using R version 3.3.1. > Besides upgrading R is not very convenient. So can you point out the > problems behind the issue? Then I'm going to fix it. > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#37 <#37>?email_source=notifications&email_token=ABJ7XWOHXR57RFTIKWU6IPLQTKGIXA5CNFSM4JL5YLXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDZ5OUQ#issuecomment-552851282>, > or unsubscribe > https://github.com/notifications/unsubscribe-auth/ABJ7XWMICYZTGGW4GA2RS3LQTKGIXANCNFSM4JL5YLXA > . > I have tried and it seems the position are all on positive strand. Below is the result: ` which(chip.data[["tags"]]$chr01 < 0) integer(0) packageVersion("spp") [1] ‘1.16.0 ’` Thanks for your help — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37?email_source=notifications&email_token=ABJ7XWKRYHYXS7KF6EEYUDDQTKJC7A5CNFSM4JL5YLXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDZ7KKI#issuecomment-552858921>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABJ7XWKQTXN7NUTZRUM2GHLQTKJC7ANCNFSM4JL5YLXA> .

[Bumblebee5k8m7]

Maybe a problem with the bsm file format? Can you show some lines from the bam file? Il mar 12 nov 2019, 12:42 Bumblebee5k8m7 notifications@github.com ha scritto:
…
https://cran.r-project.org/web/packages/spp/index.html Il mar 12 nov 2019, 12:24 Francesco Ferrari < @.*> ha scritto: … <#m_7811761540078084699_> Please try the latest spp version 1.16 Il mar 12 nov 2019, 12:18 Bumblebee5k8m7 @.> ha scritto: > The code in the warnings below shows you are using spp1.15 Please the > latest 1.16 Also use the latest R version, not the default one in centos Il > mar 12 nov 2019, 04:36 Bumblebee5k8m7 @. ha > scritto: > > Before installation I have read the dependencies: > Package: spp > Type: Package > Title: ChIP-Seq Processing Pipeline > Version: 1.15.5 > Author: Peter K > Date: 2018-07-19 > Depends: R (>= 3.3.0), Rcpp > > It seems that errors should not happen while I'm using R version 3.3.1. > Besides upgrading R is not very convenient. So can you point out the > problems behind the issue? Then I'm going to fix it. > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#37 <#37>?email_source=notifications&email_token=ABJ7XWOHXR57RFTIKWU6IPLQTKGIXA5CNFSM4JL5YLXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDZ5OUQ#issuecomment-552851282>, > or unsubscribe > https://github.com/notifications/unsubscribe-auth/ABJ7XWMICYZTGGW4GA2RS3LQTKGIXANCNFSM4JL5YLXA > . > I have tried and it seems the position are all on positive strand. Below is the result: which(chip.data[["tags"]]$chr01 < 0) integer(0) packageVersion("spp") [1] ‘1.16.0 ’ Thanks for your help — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37?email_source=notifications&email_token=ABJ7XWKRYHYXS7KF6EEYUDDQTKJC7A5CNFSM4JL5YLXKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDZ7KKI#issuecomment-552858921>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABJ7XWKQTXN7NUTZRUM2GHLQTKJC7ANCNFSM4JL5YLXA .

I run the same R commands with the same bam file on another ubuntu server. It worked! So I'm sure the problem does not stem from the bam files.
Here are the reports when I installed the spp version 1.10. It may come from the compiling process
`[hyu@localhost R]$ R CMD INSTALL spp_1.10.tar.gz

• installing to library ‘/home/hyu/R/lib64/R/library’
• installing source package ‘spp’ ...
  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 ISO C89... none needed
  checking for BZ2_bzDecompressInit in -lbz2... yes
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c BGZF.cpp -o BGZF.o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c BamAlignment.cpp -o BamAlignment.o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c BamIndex.cpp -o BamIndex.o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c BamMultiReader.cpp -o BamMultiReader. o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c BamReader.cpp -o BamReader.o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c BamReader_p.cpp -o BamReader_p.o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c BamStandardIndex_p.cpp -o BamStandard Index_p.o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c BamToolsIndex_p.cpp -o BamToolsIndex_ p.o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c BamWriter.cpp -o BamWriter.o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c BamWriter_p.cpp -o BamWriter_p.o
  g++ -I/home/hyu/R/lib64/R/include -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fpic -g -O2 -c bamread.cpp -o bamread.o
  In file included from /usr/local/include/c++/8.3.0/ext/hash_set:60,
  from pc.h:5,
  from bamread.cpp:1:
  /usr/local/include/c++/8.3.0/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be rem oved without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers a nd interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
  #warning
  ^~~~~~~
  bamread.cpp: In function ‘SEXPREC* read_bam(SEXP, SEXP)’:
  bamread.cpp:67:55: error: template argument 3 is invalid
  hash_map<string, int, hash,equal_to > cind_map;
  ^
  bamread.cpp:104:59: error: template argument 3 is invalid
  hash_map<string, int, hash,equal_to >::const_iterator li=cind_map.find(chr);
  ^
  bamread.cpp:104:77: error: qualified-id in declaration before ‘li’
  hash_map<string, int, hash,equal_to >::const_iterator li=cind_map.find(chr);
  ^~
  bamread.cpp:106:10: error: ‘li’ was not declared in this scope
  if(li==cind_map.end()) {
  ^~
  bamread.cpp:106:23: error: request for member ‘end’ in ‘cind_map’, which is of non-class type ‘int’
  if(li==cind_map.end()) {
  ^~~
  bamread.cpp:110:10: error: no match for ‘operator[]’ (operand types are ‘int’ and ‘std::__cxx11::string’ {aka ‘std::__cxx11::basic_string’})
  cind_map[chr]=cind;
  ^
  make: *** [bamread.o] Error 1
  ERROR: compilation failed for package ‘spp’
• removing ‘/home/hyu/R/lib64/R/library/spp’
• restoring previous ‘/home/hyu/R/lib64/R/library/spp’
  `