search for: getgeo

Dear R-ers, I am using getGEO to download expression data from the Gene Expression Omnibus. With default settings, when a file is downloaded and parsed, lots of dotted lines are printed in the terminal, like this: .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .....

Rusty, I currently try to make my guest boot from an virtio root device without having an external kernel. Some of the tools that I tried expect HDIO_GETGEO to work. The most interesting value is likely the geo.start value to get the offset of a partition. This value is filled by block/ioctl.c if fops->getgeo is set. This patch also fills in some standard values for heads, sectors and cylinders. Makes sense? Signed-off-by: Christian Borntraeger &l...

Rusty, I currently try to make my guest boot from an virtio root device without having an external kernel. Some of the tools that I tried expect HDIO_GETGEO to work. The most interesting value is likely the geo.start value to get the offset of a partition. This value is filled by block/ioctl.c if fops->getgeo is set. This patch also fills in some standard values for heads, sectors and cylinders. Makes sense? Signed-off-by: Christian Borntraeger &l...

Hello, I am trying to download a SOFT matrix file for GSE series to extract raw intensity data. gse<- getGEO('GSExxxx', AnnotGPL=T) However, I am not able to use the function Table(gse), which returns the following error >>>Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Table", for signature "GSE" If I try to use the...

Hi Jeremy, The below implements the getgeo hook for Xen block devices. Extracted from the xen-unstable tree where it has been used for ages. It is useful to have because it allows things like grub2 (used by the Debian installer images) to work in a guest domain without having to sprinkle Xen specific hacks around the place. Signed-off-by:...

Hi Jeremy, The below implements the getgeo hook for Xen block devices. Extracted from the xen-unstable tree where it has been used for ages. It is useful to have because it allows things like grub2 (used by the Debian installer images) to work in a guest domain without having to sprinkle Xen specific hacks around the place. Signed-off-by:...

some time ago i communicated the same issue to sean, and i'm very glad he has improved the package -- thanks! i'm purposefully posting to r-devel rather than to bioconductor. i think that download.file could be improved to avoid this sort of spamming output seen previously with getGEO. currently, it prints dots (when it does) in 5 10-packs per line, line after line. instead, it could be repeatedly printing them on the same line, to give it a more progress bar-like look. the function putdots (src/modules/internet/internet.c:218) is responsible for printing the dots. after eac...

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Hola, buenas tardes, Hace unos dias que intento cargar unos datos de microarrays del ncbi con versión de R 2.15.2 de 32 bits en windows xp. he utilizado el siguiente codigo: library(Biobase) library(GEOquery) library(limma) gset <- getGEO("GSE6536", GSEMatrix =TRUE) Al hacerlo me da este error: "Error in function (type, msg, asError = TRUE) : couldn't connect to host" Como no podía cargar los datos directamente, me descargué el archivo y al intentarlo cargar desde el ordenador me sale otro error: Error:...

...7 files changed, 142 insertions(+), 204 deletions(-) > > diff --git a/drivers/block/virtio_blk.c b/drivers/block/virtio_blk.c > index 7ffd719d89de..fbbf18ac1d5d 100644 > --- a/drivers/block/virtio_blk.c > +++ b/drivers/block/virtio_blk.c > @@ -405,6 +405,9 @@ static int virtblk_getgeo(struct block_device *bd, struct hd_geometry *geo) > > static const struct block_device_operations virtblk_fops = { > .ioctl = virtblk_ioctl, > +#ifdef CONFIG_COMPAT > + .compat_ioctl = blkdev_compat_ptr_ioctl, > +#endif > .owner = THIS_MODULE, > .getgeo = virtblk_...

...7 files changed, 142 insertions(+), 204 deletions(-) > > diff --git a/drivers/block/virtio_blk.c b/drivers/block/virtio_blk.c > index 7ffd719d89de..fbbf18ac1d5d 100644 > --- a/drivers/block/virtio_blk.c > +++ b/drivers/block/virtio_blk.c > @@ -405,6 +405,9 @@ static int virtblk_getgeo(struct block_device *bd, struct hd_geometry *geo) > > static const struct block_device_operations virtblk_fops = { > .ioctl = virtblk_ioctl, > +#ifdef CONFIG_COMPAT > + .compat_ioctl = blkdev_compat_ptr_ioctl, > +#endif > .owner = THIS_MODULE, > .getgeo = virtblk_...

A userspace process holding a file descriptor to a virtio_blk device can still invoke block_device_operations after hot unplug. This leads to a use-after-free accessing vblk->vdev in virtblk_getgeo() when ioctl(HDIO_GETGEO) is invoked: BUG: unable to handle kernel NULL pointer dereference at 0000000000000090 IP: [<ffffffffc00e5450>] virtio_check_driver_offered_feature+0x10/0x90 [virtio] PGD 800000003a92f067 PUD 3a930067 PMD 0 Oops: 0000 [#1] SMP CPU: 0 PID: 1310 Comm: hdio-ge...

A userspace process holding a file descriptor to a virtio_blk device can still invoke block_device_operations after hot unplug. This leads to a use-after-free accessing vblk->vdev in virtblk_getgeo() when ioctl(HDIO_GETGEO) is invoked: BUG: unable to handle kernel NULL pointer dereference at 0000000000000090 IP: [<ffffffffc00e5450>] virtio_check_driver_offered_feature+0x10/0x90 [virtio] PGD 800000003a92f067 PUD 3a930067 PMD 0 Oops: 0000 [#1] SMP CPU: 0 PID: 1310 Comm: hdio-ge...

A userspace process holding a file descriptor to a virtio_blk device can still invoke block_device_operations after hot unplug. This leads to a use-after-free accessing vblk->vdev in virtblk_getgeo() when ioctl(HDIO_GETGEO) is invoked: BUG: unable to handle kernel NULL pointer dereference at 0000000000000090 IP: [<ffffffffc00e5450>] virtio_check_driver_offered_feature+0x10/0x90 [virtio] PGD 800000003a92f067 PUD 3a930067 PMD 0 Oops: 0000 [#1] SMP CPU: 0 PID: 1310 Comm: hdio-ge...

A userspace process holding a file descriptor to a virtio_blk device can still invoke block_device_operations after hot unplug. This leads to a use-after-free accessing vblk->vdev in virtblk_getgeo() when ioctl(HDIO_GETGEO) is invoked: BUG: unable to handle kernel NULL pointer dereference at 0000000000000090 IP: [<ffffffffc00e5450>] virtio_check_driver_offered_feature+0x10/0x90 [virtio] PGD 800000003a92f067 PUD 3a930067 PMD 0 Oops: 0000 [#1] SMP CPU: 0 PID: 1310 Comm: hdio-ge...

A userspace process holding a file descriptor to a virtio_blk device can still invoke block_device_operations after hot unplug. For example, a program that has /dev/vdb open can call ioctl(HDIO_GETGEO) after hot unplug to invoke virtblk_getgeo(). Introduce a reference count in struct virtio_blk so that its lifetime covers both virtio_driver probe/remove and block_device_operations open/release users. This ensures that block_device_operations functions like virtblk_getgeo() can safely access st...

A userspace process holding a file descriptor to a virtio_blk device can still invoke block_device_operations after hot unplug. For example, a program that has /dev/vdb open can call ioctl(HDIO_GETGEO) after hot unplug to invoke virtblk_getgeo(). Introduce a reference count in struct virtio_blk so that its lifetime covers both virtio_driver probe/remove and block_device_operations open/release users. This ensures that block_device_operations functions like virtblk_getgeo() can safely access st...

On Wed, Apr 29, 2020 at 05:53:45PM +0100, Stefan Hajnoczi wrote: > A userspace process holding a file descriptor to a virtio_blk device can > still invoke block_device_operations after hot unplug. This leads to a > use-after-free accessing vblk->vdev in virtblk_getgeo() when > ioctl(HDIO_GETGEO) is invoked: > > BUG: unable to handle kernel NULL pointer dereference at 0000000000000090 > IP: [<ffffffffc00e5450>] virtio_check_driver_offered_feature+0x10/0x90 [virtio] > PGD 800000003a92f067 PUD 3a930067 PMD 0 > Oops: 0000 [#1] SMP &g...

...n Hajnoczi <stefanha at redhat.com> [ Upstream commit 90b5feb8c4bebc76c27fcaf3e1a0e5ca2d319e9e ] A userspace process holding a file descriptor to a virtio_blk device can still invoke block_device_operations after hot unplug. This leads to a use-after-free accessing vblk->vdev in virtblk_getgeo() when ioctl(HDIO_GETGEO) is invoked: BUG: unable to handle kernel NULL pointer dereference at 0000000000000090 IP: [<ffffffffc00e5450>] virtio_check_driver_offered_feature+0x10/0x90 [virtio] PGD 800000003a92f067 PUD 3a930067 PMD 0 Oops: 0000 [#1] SMP CPU: 0 PID: 1310 Comm: hdio-ge...

...n Hajnoczi <stefanha at redhat.com> [ Upstream commit 90b5feb8c4bebc76c27fcaf3e1a0e5ca2d319e9e ] A userspace process holding a file descriptor to a virtio_blk device can still invoke block_device_operations after hot unplug. This leads to a use-after-free accessing vblk->vdev in virtblk_getgeo() when ioctl(HDIO_GETGEO) is invoked: BUG: unable to handle kernel NULL pointer dereference at 0000000000000090 IP: [<ffffffffc00e5450>] virtio_check_driver_offered_feature+0x10/0x90 [virtio] PGD 800000003a92f067 PUD 3a930067 PMD 0 Oops: 0000 [#1] SMP CPU: 0 PID: 1310 Comm: hdio-ge...