From bbo|ker @end|ng |rom gm@||@com  Sun May  5 18:18:07 2019
From: bbo|ker @end|ng |rom gm@||@com (Ben Bolker)
Date: Sun, 5 May 2019 12:18:07 -0400
Subject: [Rd] Staged installation fail on some file systems
In-Reply-To: <CAFDcVCTYc53f9COpNoeqbYGxWOE_CCrAbCiStDpo6YBmXG6Txg@mail.gmail.com>
References: <CAFDcVCTYc53f9COpNoeqbYGxWOE_CCrAbCiStDpo6YBmXG6Txg@mail.gmail.com>
Message-ID: <8862a020-1378-4ba4-885b-0dd34f1e95d7@gmail.com>


  This happens to me, too, on an Ubuntu virtual machine (with a "vboxsf"
file system, over an underlying MacOS (HFS) file system), but only when
installing as part of R CMD check ... I did find the workaround, so I
don't think I reported it before.

On 2019-05-04 10:35 p.m., Henrik Bengtsson wrote:
> I'm observing that the new staged installation in R 3.6.0 can produce:
> 
> mv: cannot move
> ?/home/alice/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-codetools/00new/codetools?
> to ?/home/alice/R/x86_64-pc-linux-gnu-library/3.6/codetools?: File
> exists
> ERROR:   moving to final location failed
> 
> on some file systems.
> 
> # EXAMPLE
> 
> $ R --vanilla
> R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
> Copyright (C) 2019 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
> ...
> 
>> install.packages("codetools", repos="https://cran.r-project.org")
> Installing package into ?/wynton/home/cbi/hb/R/x86_64-pc-linux-gnu-library/3.6?
> (as ?lib? is unspecified)
> trying URL 'https://cran.r-project.org/src/contrib/codetools_0.2-16.tar.gz'
> Content type 'application/x-gzip' length 12996 bytes (12 KB)
> ==================================================
> downloaded 12 KB
> 
> * installing *source* package ?codetools? ...
> ** package ?codetools? successfully unpacked and MD5 sums checked
> ** using staged installation
> ** R
> ** byte-compile and prepare package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded from temporary location
> mv: cannot move
> ?/home/alice/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-codetools/00new/codetools?
> to ?/home/alice/R/x86_64-pc-linux-gnu-library/3.6/codetools?: File
> exists
> ERROR:   moving to final location failed
> * removing ?/home/alice/R/x86_64-pc-linux-gnu-library/3.6/codetools?
> 
> The downloaded source packages are in
> ?/scratch/alice/Rtmp6UYDzu/downloaded_packages?
> Warning message:
> In install.packages("codetools", repos = "https://cran.r-project.org") :
> installation of package ?codetools? had non-zero exit status
> 
> 
> # WORKAROUND
> 
> Disabling staged installation, for instance by setting environment
> variable 'R_INSTALL_STAGED=false' avoids this problem.
> 
> 
> # TROUBLESHOOTING
> 
> I think it comes down to the following call in src/library/tools/R/install.R:
> 
>   status <- system(paste("mv -f",
>                          shQuote(instdir),
>                          shQuote(dirname(final_instdir))))
> 
> https://github.com/wch/r-source/blob/d253331f578814f919f150ffdf1fe581618079a3/src/library/tools/R/install.R#L1645-L1647
> 
> which effectively does:
> 
> $ mkdir -p path/pkg  ## empty final destination placeholder(?)
> $ mkdir -p path/to/pkg
> $ mv -f path/to/pkg path
> 
> However, on one (and only one) of several systems I've tested, that
> 'mv' produce the error:
> 
>   mv: cannot move ?path/to/pkg? to ?path/pkg?: File exists
> 
> This is on a BeeGFS parallel file system.  I cannot tell if that 'mv
> -f' should work or not, or if it is even well defined.  FWIW, the
> above 'mv' does indeed work if I switch to another folder that is
> mounted on a different, NFS, file system, i.e. it is not kernel/OS
> specific (here CentOS 7.6.1810).
> 
> If of any use, here's the 'strace' of the above 'mv':
> 
> $ strace mv -f path/to/pkg path
> execve("/usr/bin/mv", ["mv", "-f", "path/to/pkg", "path"], [/* 118 vars */]) = 0
> brk(NULL)                               = 0xcf3000
> mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1,
> 0) = 0x7fde2ceb1000
> access("/etc/ld.so.preload", R_OK)      = -1 ENOENT (No such file or directory)
> open("/usr/lib64/openmpi/lib/tls/x86_64/libselinux.so.1",
> O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
> stat("/usr/lib64/openmpi/lib/tls/x86_64", 0x7ffc6a3fb170) = -1 ENOENT
> (No such file or directory)
> open("/usr/lib64/openmpi/lib/tls/libselinux.so.1", O_RDONLY|O_CLOEXEC)
> = -1 ENOENT (No such file or directory)
> stat("/usr/lib64/openmpi/lib/tls", 0x7ffc6a3fb170) = -1 ENOENT (No
> such file or directory)
> open("/usr/lib64/openmpi/lib/x86_64/libselinux.so.1",
> O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
> stat("/usr/lib64/openmpi/lib/x86_64", 0x7ffc6a3fb170) = -1 ENOENT (No
> such file or directory)
> open("/usr/lib64/openmpi/lib/libselinux.so.1", O_RDONLY|O_CLOEXEC) =
> -1 ENOENT (No such file or directory)
> stat("/usr/lib64/openmpi/lib", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
> open("/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 3
> fstat(3, {st_mode=S_IFREG|0644, st_size=96960, ...}) = 0
> mmap(NULL, 96960, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7fde2ce99000
> close(3)                                = 0
> open("/lib64/libselinux.so.1", O_RDONLY|O_CLOEXEC) = 3
> read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\320i\0\0\0\0\0\0"...,
> 832) = 832
> fstat(3, {st_mode=S_IFREG|0755, st_size=155784, ...}) = 0
> mmap(NULL, 2255184, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3,
> 0) = 0x7fde2ca6a000
> mprotect(0x7fde2ca8e000, 2093056, PROT_NONE) = 0
> mmap(0x7fde2cc8d000, 8192, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x23000) = 0x7fde2cc8d000
> mmap(0x7fde2cc8f000, 6480, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7fde2cc8f000
> close(3)                                = 0
> open("/usr/lib64/openmpi/lib/libacl.so.1", O_RDONLY|O_CLOEXEC) = -1
> ENOENT (No such file or directory)
> open("/lib64/libacl.so.1", O_RDONLY|O_CLOEXEC) = 3
> read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\200\37\0\0\0\0\0\0"...,
> 832) = 832
> fstat(3, {st_mode=S_IFREG|0755, st_size=37056, ...}) = 0
> mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1,
> 0) = 0x7fde2ce98000
> mmap(NULL, 2130560, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3,
> 0) = 0x7fde2c861000
> mprotect(0x7fde2c868000, 2097152, PROT_NONE) = 0
> mmap(0x7fde2ca68000, 8192, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x7000) = 0x7fde2ca68000
> close(3)                                = 0
> open("/usr/lib64/openmpi/lib/libattr.so.1", O_RDONLY|O_CLOEXEC) = -1
> ENOENT (No such file or directory)
> open("/lib64/libattr.so.1", O_RDONLY|O_CLOEXEC) = 3
> read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\320\23\0\0\0\0\0\0"...,
> 832) = 832
> fstat(3, {st_mode=S_IFREG|0755, st_size=19896, ...}) = 0
> mmap(NULL, 2113904, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3,
> 0) = 0x7fde2c65c000
> mprotect(0x7fde2c660000, 2093056, PROT_NONE) = 0
> mmap(0x7fde2c85f000, 8192, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x3000) = 0x7fde2c85f000
> close(3)                                = 0
> open("/usr/lib64/openmpi/lib/libc.so.6", O_RDONLY|O_CLOEXEC) = -1
> ENOENT (No such file or directory)
> open("/lib64/libc.so.6", O_RDONLY|O_CLOEXEC) = 3
> read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\340$\2\0\0\0\0\0"...,
> 832) = 832
> fstat(3, {st_mode=S_IFREG|0755, st_size=2151672, ...}) = 0
> mmap(NULL, 3981792, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3,
> 0) = 0x7fde2c28f000
> mprotect(0x7fde2c451000, 2097152, PROT_NONE) = 0
> mmap(0x7fde2c651000, 24576, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x1c2000) = 0x7fde2c651000
> mmap(0x7fde2c657000, 16864, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7fde2c657000
> close(3)                                = 0
> open("/usr/lib64/openmpi/lib/libpcre.so.1", O_RDONLY|O_CLOEXEC) = -1
> ENOENT (No such file or directory)
> open("/lib64/libpcre.so.1", O_RDONLY|O_CLOEXEC) = 3
> read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\360\25\0\0\0\0\0\0"...,
> 832) = 832
> fstat(3, {st_mode=S_IFREG|0755, st_size=402384, ...}) = 0
> mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1,
> 0) = 0x7fde2ce97000
> mmap(NULL, 2494984, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3,
> 0) = 0x7fde2c02d000
> mprotect(0x7fde2c08d000, 2097152, PROT_NONE) = 0
> mmap(0x7fde2c28d000, 8192, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x60000) = 0x7fde2c28d000
> close(3)                                = 0
> open("/usr/lib64/openmpi/lib/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1
> ENOENT (No such file or directory)
> open("/lib64/libdl.so.2", O_RDONLY|O_CLOEXEC) = 3
> read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\220\r\0\0\0\0\0\0"...,
> 832) = 832
> fstat(3, {st_mode=S_IFREG|0755, st_size=19288, ...}) = 0
> mmap(NULL, 2109712, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3,
> 0) = 0x7fde2be29000
> mprotect(0x7fde2be2b000, 2097152, PROT_NONE) = 0
> mmap(0x7fde2c02b000, 8192, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x2000) = 0x7fde2c02b000
> close(3)                                = 0
> open("/usr/lib64/openmpi/lib/libpthread.so.0", O_RDONLY|O_CLOEXEC) =
> -1 ENOENT (No such file or directory)
> open("/lib64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = 3
> read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\260l\0\0\0\0\0\0"...,
> 832) = 832
> fstat(3, {st_mode=S_IFREG|0755, st_size=141968, ...}) = 0
> mmap(NULL, 2208904, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3,
> 0) = 0x7fde2bc0d000
> mprotect(0x7fde2bc24000, 2093056, PROT_NONE) = 0
> mmap(0x7fde2be23000, 8192, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x16000) = 0x7fde2be23000
> mmap(0x7fde2be25000, 13448, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7fde2be25000
> close(3)                                = 0
> mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1,
> 0) = 0x7fde2ce96000
> mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1,
> 0) = 0x7fde2ce94000
> arch_prctl(ARCH_SET_FS, 0x7fde2ce94840) = 0
> mprotect(0x7fde2c651000, 16384, PROT_READ) = 0
> mprotect(0x7fde2be23000, 4096, PROT_READ) = 0
> mprotect(0x7fde2c02b000, 4096, PROT_READ) = 0
> mprotect(0x7fde2c28d000, 4096, PROT_READ) = 0
> mprotect(0x7fde2c85f000, 4096, PROT_READ) = 0
> mprotect(0x7fde2ca68000, 4096, PROT_READ) = 0
> mprotect(0x7fde2cc8d000, 4096, PROT_READ) = 0
> mprotect(0x61d000, 4096, PROT_READ)     = 0
> mprotect(0x7fde2ceb2000, 4096, PROT_READ) = 0
> munmap(0x7fde2ce99000, 96960)           = 0
> set_tid_address(0x7fde2ce94b10)         = 85521
> set_robust_list(0x7fde2ce94b20, 24)     = 0
> rt_sigaction(SIGRTMIN, {0x7fde2bc13790, [], SA_RESTORER|SA_SIGINFO,
> 0x7fde2bc1c5d0}, NULL, 8) = 0
> rt_sigaction(SIGRT_1, {0x7fde2bc13820, [],
> SA_RESTORER|SA_RESTART|SA_SIGINFO, 0x7fde2bc1c5d0}, NULL, 8) = 0
> rt_sigprocmask(SIG_UNBLOCK, [RTMIN RT_1], NULL, 8) = 0
> getrlimit(RLIMIT_STACK, {rlim_cur=8192*1024, rlim_max=RLIM64_INFINITY}) = 0
> statfs("/sys/fs/selinux", {f_type=SELINUX_MAGIC, f_bsize=4096,
> f_blocks=0, f_bfree=0, f_bavail=0, f_files=0, f_ffree=0, f_fsid={0,
> 0}, f_namelen=255, f_frsize=4096, f_flags=ST_VALID|ST_RELATIME}) = 0
> statfs("/sys/fs/selinux", {f_type=SELINUX_MAGIC, f_bsize=4096,
> f_blocks=0, f_bfree=0, f_bavail=0, f_files=0, f_ffree=0, f_fsid={0,
> 0}, f_namelen=255, f_frsize=4096, f_flags=ST_VALID|ST_RELATIME}) = 0
> stat("/sys/fs/selinux", {st_mode=S_IFDIR|0755, st_size=0, ...}) = 0
> brk(NULL)                               = 0xcf3000
> brk(0xd14000)                           = 0xd14000
> access("/etc/selinux/config", F_OK)     = 0
> open("/usr/lib/locale/locale-archive", O_RDONLY|O_CLOEXEC) = 3
> fstat(3, {st_mode=S_IFREG|0644, st_size=106075056, ...}) = 0
> mmap(NULL, 106075056, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7fde256e3000
> close(3)                                = 0
> geteuid()                               = 34002
> ioctl(0, TCGETS, {B38400 opost isig icanon echo ...}) = 0
> stat("path", {st_mode=S_IFDIR|0755, st_size=2, ...}) = 0
> lstat("path/to/pkg", {st_mode=S_IFDIR|0755, st_size=0, ...}) = 0
> lstat("path/pkg", {st_mode=S_IFDIR|0755, st_size=0, ...}) = 0
> renameat2(AT_FDCWD, "path/to/pkg", AT_FDCWD, "path/pkg", 0) = -1
> EEXIST (File exists)
> open("/usr/share/locale/locale.alias", O_RDONLY|O_CLOEXEC) = 3
> fstat(3, {st_mode=S_IFREG|0644, st_size=2502, ...}) = 0
> mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1,
> 0) = 0x7fde2ceb0000
> read(3, "# Locale name alias data base.\n#"..., 4096) = 2502
> read(3, "", 4096)                       = 0
> close(3)                                = 0
> munmap(0x7fde2ceb0000, 4096)            = 0
> open("/usr/share/locale/en_US.UTF-8/LC_MESSAGES/coreutils.mo",
> O_RDONLY) = -1 ENOENT (No such file or directory)
> open("/usr/share/locale/en_US.utf8/LC_MESSAGES/coreutils.mo",
> O_RDONLY) = -1 ENOENT (No such file or directory)
> open("/usr/share/locale/en_US/LC_MESSAGES/coreutils.mo", O_RDONLY) =
> -1 ENOENT (No such file or directory)
> open("/usr/share/locale/en.UTF-8/LC_MESSAGES/coreutils.mo", O_RDONLY)
> = -1 ENOENT (No such file or directory)
> open("/usr/share/locale/en.utf8/LC_MESSAGES/coreutils.mo", O_RDONLY) =
> -1 ENOENT (No such file or directory)
> open("/usr/share/locale/en/LC_MESSAGES/coreutils.mo", O_RDONLY) = -1
> ENOENT (No such file or directory)
> open("/usr/lib64/charset.alias", O_RDONLY|O_NOFOLLOW) = -1 ENOENT (No
> such file or directory)
> write(2, "mv: ", 4mv: )                     = 4
> write(2, "cannot move \342\200\230path/to/pkg\342\200\231 to"...,
> 47cannot move ?path/to/pkg? to ?path/pkg?) = 47
> open("/usr/share/locale/en_US.UTF-8/LC_MESSAGES/libc.mo", O_RDONLY) =
> -1 ENOENT (No such file or directory)
> open("/usr/share/locale/en_US.utf8/LC_MESSAGES/libc.mo", O_RDONLY) =
> -1 ENOENT (No such file or directory)
> open("/usr/share/locale/en_US/LC_MESSAGES/libc.mo", O_RDONLY) = -1
> ENOENT (No such file or directory)
> open("/usr/share/locale/en.UTF-8/LC_MESSAGES/libc.mo", O_RDONLY) = -1
> ENOENT (No such file or directory)
> open("/usr/share/locale/en.utf8/LC_MESSAGES/libc.mo", O_RDONLY) = -1
> ENOENT (No such file or directory)
> open("/usr/share/locale/en/LC_MESSAGES/libc.mo", O_RDONLY) = -1 ENOENT
> (No such file or directory)
> write(2, ": File exists", 13: File exists)           = 13
> write(2, "\n", 1
> )                       = 1
> lseek(0, 0, SEEK_CUR)                   = -1 ESPIPE (Illegal seek)
> close(0)                                = 0
> close(1)                                = 0
> close(2)                                = 0
> exit_group(1)                           = ?
> +++ exited with 1 +++
> 
> /Henrik
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] Staged installation fail on some file systems
Ben Bolker