similar to: Suppress output from getGEO

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

Dear R helpers   I am calculating the 'Yield to Maturity' for the Bond with following characteristics.   Its a $1000 face value, 3 year bond with 10% annual coupon and is priced at 101. The yield to maturity can be calculated after solving the equation -   1010 = [100 / (1+ytm)]  + [100 / (1+ytm)^2] + [ 1100 / (1 + ytm)^3]   This can be solved by trial and error method s.t. ytm = 9.601%.

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

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

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Dear list, I am trying to construct a list of functions using rep. I can't understand the following: > c(character, character) => list with two functions > rep(character, 2) => error The error says that "object of type 'special' is not subsettable", and I have no idea what this means. Would you please help me. The purpose of doing the above is that I

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

R-developers, I'm looking for some 'best practices', or perhaps an upstream solution (I have a deja vu about this, so sorry if it's already been asked). Problems occur when a file is encoded as latin1, but the user has a UTF-8 locale (or I guess more generally when the input locale does not match R's). Here are two examples from the Bioconductor help list:

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: Ian Campbell <ijc@hellion.org.uk> diff --git

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: Ian Campbell <ijc@hellion.org.uk> diff --git

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

Hi, all I met a problem to query GSE3524, which cannot be open on my computer. I hope some of you would be kind to give me some advice. Thanks! The code is as follow: ################## library(GEOquery) gsename="GSE3524" gse=getGEO(gsename) ################## The error information follows as

Hi all, I am trying to install the package "GEOquery" in unix. I have downloaded the standard version of R and this package is not contained in the default. I know that I can select repositories under windows but I don't know how to do it in unix. Does anyone have any idea on this? Thank you in advance, Eleni [[alternative HTML version deleted]]

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

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

On Wed, Dec 11, 2019 at 09:42:49PM +0100, Arnd Bergmann wrote: > Each driver calling scsi_ioctl() gets an equivalent compat_ioctl() > handler that implements the same commands by calling scsi_compat_ioctl(). > > The scsi_cmd_ioctl() and scsi_cmd_blk_ioctl() functions are compatible > at this point, so any driver that calls those can do so for both native > and compat mode, with

On Wed, Dec 11, 2019 at 09:42:49PM +0100, Arnd Bergmann wrote: > Each driver calling scsi_ioctl() gets an equivalent compat_ioctl() > handler that implements the same commands by calling scsi_compat_ioctl(). > > The scsi_cmd_ioctl() and scsi_cmd_blk_ioctl() functions are compatible > at this point, so any driver that calls those can do so for both native > and compat mode, with

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

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

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