[Rd] Staged installation fail on some file systems
Henrik Bengtsson
henr|k@bengt@@on @end|ng |rom gm@||@com
Sun May 5 04:35:27 CEST 2019
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
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